changeset 3:bf9bd980f729 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 19:10:16 +0000
parents d2c1c85b8867
children 1533239ed6f2
files 404-urls.patch CometAdapter.xml filetypes.txt generate-foo.sh generate.sh hardcoded_params.json macros.xml macros_autotest.xml macros_test.xml prepare_test_data.sh prepare_test_data_manual.sh test-data.sh tools_blacklist.txt
diffstat 13 files changed, 2464 insertions(+), 2181 deletions(-) [+]
line wrap: on
line diff
--- a/404-urls.patch	Wed Sep 23 13:43:34 2020 +0000
+++ b/404-urls.patch	Tue Oct 13 19:10:16 2020 +0000
@@ -1,65 +1,11 @@
-diff -ruN ClusterMassTracesByPrecursor.xml ClusterMassTracesByPrecursor.xml
---- ClusterMassTracesByPrecursor.xml	2020-09-21 17:02:36.060104555 +0200
-+++ ClusterMassTracesByPrecursor.xml	2020-09-21 17:00:02.864815223 +0200
-@@ -75,8 +75,6 @@
-     <expand macro="manutest_ClusterMassTracesByPrecursor"/>
-   </tests>
-   <help><![CDATA[Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile.
--
--
--For more information, visit http://www.openms.de/documentation/UTILS_ClusterMassTracesByPrecursor.html]]></help>
-+]]></help>
-   <expand macro="references"/>
- </tool>
-diff -ruN ClusterMassTraces.xml ClusterMassTraces.xml
---- ClusterMassTraces.xml	2020-09-21 17:02:36.060104555 +0200
-+++ ClusterMassTraces.xml	2020-09-21 17:00:22.192722036 +0200
-@@ -69,8 +69,6 @@
-     <expand macro="manutest_ClusterMassTraces"/>
-   </tests>
-   <help><![CDATA[Creates pseudo spectra.
--
--
--For more information, visit http://www.openms.de/documentation/UTILS_ClusterMassTraces.html]]></help>
-+]]></help>
+diff -ruN FeatureFinderSuperHirn.xml FeatureFinderSuperHirn.xml
+--- FeatureFinderSuperHirn.xml	2020-10-02 12:06:56.398572301 +0200
++++ FeatureFinderSuperHirn.xml	2020-10-02 12:07:31.511153834 +0200
+@@ -105,6 +105,6 @@
+   <help><![CDATA[Finds mass spectrometric features in mass spectra.
+ 
+ 
+-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FeatureFinderSuperHirn.html]]></help>
++For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.6.0/html/UTILS_FeatureFinderSuperHirn.html]]></help>
    <expand macro="references"/>
  </tool>
-diff -ruN FeatureFinderSuperHirn.xml FeatureFinderSuperHirn.xml
---- FeatureFinderSuperHirn.xml	2020-09-21 17:02:36.060104555 +0200
-+++ FeatureFinderSuperHirn.xml	2020-09-21 17:00:42.372625907 +0200
-@@ -103,8 +103,6 @@
-     <expand macro="manutest_FeatureFinderSuperHirn"/>
-   </tests>
-   <help><![CDATA[Finds mass spectrometric features in mass spectra.
--
--
--For more information, visit http://www.openms.de/documentation/TOPP_FeatureFinderSuperHirn.html]]></help>
-+]]></help>
-   <expand macro="references"/>
- </tool>
-diff -ruN MSFraggerAdapter.xml MSFraggerAdapter.xml
---- MSFraggerAdapter.xml	2020-09-21 17:02:36.060104555 +0200
-+++ MSFraggerAdapter.xml	2020-09-21 17:01:04.892519985 +0200
-@@ -250,8 +250,6 @@
-     <expand macro="manutest_MSFraggerAdapter"/>
-   </tests>
-   <help><![CDATA[Peptide Identification with MSFragger
--
--
--For more information, visit http://www.openms.de/documentation/UTILS_MSFraggerAdapter.html]]></help>
-+]]></help>
-   <expand macro="references"/>
- </tool>
-diff -ruN SimpleSearchEngine.xml SimpleSearchEngine.xml
---- SimpleSearchEngine.xml	2020-09-21 17:02:36.060104555 +0200
-+++ SimpleSearchEngine.xml	2020-09-21 17:01:33.020389600 +0200
-@@ -5373,8 +5373,6 @@
-     <expand macro="manutest_SimpleSearchEngine"/>
-   </tests>
-   <help><![CDATA[Annotates MS/MS spectra using SimpleSearchEngine.
--
--
--For more information, visit http://www.openms.de/documentation/UTILS_SimpleSearchEngine.html]]></help>
-+]]></help>
-   <expand macro="references"/>
- </tool>
--- a/CometAdapter.xml	Wed Sep 23 13:43:34 2020 +0000
+++ b/CometAdapter.xml	Tue Oct 13 19:10:16 2020 +0000
@@ -63,12 +63,12 @@
 #end if]]></command>
   <configfiles>
     <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"comet_executable": "comet", "comet_version": "2016.01 rev. 3", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+    <configfile name="hardcoded_json"><![CDATA[{"comet_executable": "comet", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
     <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/>
     <param name="database" argument="-database" type="data" format="fasta" optional="false" label="FASTA file" help=" select fasta data sets(s)"/>
-    <param name="default_params_file" argument="-default_params_file" type="data" format="txt" optional="true" label="Default Comet params file" help="All parameters of this take precedence. A template file can be generated using comet.exe -p select txt data sets(s)"/>
+    <param name="default_params_file" argument="-default_params_file" type="data" format="txt" optional="true" label="Default Comet params file" help="All parameters of this take precedence. A template file can be generated using 'comet.exe -p' select txt data sets(s)"/>
     <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor monoisotopic mass tolerance (Comet parameter: peptide_mass_tolerance)" help="See also precursor_error_units to set the unit"/>
     <param name="precursor_error_units" argument="-precursor_error_units" display="radio" type="select" optional="false" label="Unit of precursor monoisotopic mass tolerance for parameter precursor_mass_tolerance (Comet parameter: peptide_mass_units)" help="">
       <option value="amu">amu</option>
@@ -80,13 +80,25 @@
       <option value="off" selected="true">off</option>
       <option value="0/1">0/1</option>
       <option value="0/1/2">0/1/2</option>
-      <option value="-1/0/1/2/3">-1/0/1/2/3</option>
+      <option value="0/1/2/3">0/1/2/3</option>
       <option value="-8/-4/0/4/8">-8/-4/0/4/8</option>
       <expand macro="list_string_san"/>
     </param>
+    <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" min="0.0001" value="0.01" label="This is half the bin size, which is used to segment the MS/MS spectrum" help="Thus, the value should be a bit higher than for other search engines, since the bin might not be centered around the peak apex (see 'fragment_bin_offset').CAUTION: Low tolerances have heavy impact on RAM usage (since Comet uses a lot of bins in this case). Consider using use_sparse_matrix and/or spectrum_batch_size"/>
+    <param name="fragment_error_units" argument="-fragment_error_units" display="radio" type="select" optional="false" label="Fragment monoisotopic mass error units" help="">
+      <option value="Da" selected="true">Da</option>
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="fragment_bin_offset" argument="-fragment_bin_offset" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Offset of fragment bins" help="Recommended by Comet: low-res: 0.4, high-res: 0.0"/>
+    <param name="instrument" argument="-instrument" display="radio" type="select" optional="false" label="Comets theoretical_fragment_ions parameter: theoretical fragment ion peak representation, high-res: sum of intensities plus flanking bins, ion trap (low-res) ms/ms: sum of intensities of central M bin only" help="">
+      <option value="low_res">low_res</option>
+      <option value="high_res" selected="true">high_res</option>
+      <expand macro="list_string_san"/>
+    </param>
     <param name="enzyme" argument="-enzyme" type="select" optional="false" label="The enzyme used for peptide digestion" help="">
-      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+      <option value="Arg-C">Arg-C</option>
       <option value="Asp-N">Asp-N</option>
+      <option value="Trypsin" selected="true">Trypsin</option>
       <option value="unspecific cleavage">unspecific cleavage</option>
       <option value="Chymotrypsin">Chymotrypsin</option>
       <option value="CNBr">CNBr</option>
@@ -94,8 +106,7 @@
       <option value="Lys-N">Lys-N</option>
       <option value="PepsinA">PepsinA</option>
       <option value="Trypsin/P">Trypsin/P</option>
-      <option value="Arg-C">Arg-C</option>
-      <option value="Trypsin" selected="true">Trypsin</option>
+      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
       <expand macro="list_string_san"/>
     </param>
     <param name="num_enzyme_termini" argument="-num_enzyme_termini" display="radio" type="select" optional="false" label="Specify the termini where the cleavage rule has to match" help="">
@@ -105,8 +116,10 @@
       <option value="N-term unspecific">N-term unspecific</option>
       <expand macro="list_string_san"/>
     </param>
-    <param name="allowed_missed_cleavages" argument="-allowed_missed_cleavages" type="integer" optional="true" min="0" max="5" value="0" label="Number of possible cleavage sites missed by the enzyme" help="It has no effect if enzyme is unspecific cleavage"/>
-    <param name="num_hits" argument="-num_hits" type="integer" optional="true" value="5" label="Number of peptide hits in output file" help=""/>
+    <param name="missed_cleavages" argument="-missed_cleavages" type="integer" optional="true" min="0" max="5" value="1" label="Number of possible cleavage sites missed by the enzyme" help="It has no effect if enzyme is unspecific cleavage"/>
+    <param name="min_peptide_length" argument="-min_peptide_length" type="integer" optional="true" min="5" max="63" value="5" label="Minimum peptide length to conside" help=""/>
+    <param name="max_peptide_length" argument="-max_peptide_length" type="integer" optional="true" min="5" max="63" value="63" label="Maximum peptide length to conside" help=""/>
+    <param name="num_hits" argument="-num_hits" type="integer" optional="true" value="1" label="Number of peptide hits in output file" help=""/>
     <param name="precursor_charge" argument="-precursor_charge" type="text" optional="true" value="0:0" label="Precursor charge range to search (if spectrum is not annotated with a charge or if override_charge!=keep any known): 0:[num] == search all charges, 2:6 == from +2 to +6, 3:3 == +3" help="">
       <expand macro="list_string_san"/>
     </param>
@@ -157,6 +170,7 @@
       <option value="Acetyl (K)">Acetyl (K)</option>
       <option value="Acetyl (N-term)">Acetyl (N-term)</option>
       <option value="Acetyl (Protein N-term)">Acetyl (Protein N-term)</option>
+      <option value="Acetyl (R)">Acetyl (R)</option>
       <option value="Acetyl (S)">Acetyl (S)</option>
       <option value="Acetyl (T)">Acetyl (T)</option>
       <option value="Acetyl (Y)">Acetyl (Y)</option>
@@ -188,6 +202,7 @@
       <option value="AEC-MAEC (T)">AEC-MAEC (T)</option>
       <option value="AEC-MAEC:2H(4) (S)">AEC-MAEC:2H(4) (S)</option>
       <option value="AEC-MAEC:2H(4) (T)">AEC-MAEC:2H(4) (T)</option>
+      <option value="AFB1_Dialdehyde (K)">AFB1_Dialdehyde (K)</option>
       <option value="AHA-Alkyne (M)">AHA-Alkyne (M)</option>
       <option value="AHA-Alkyne-KDDDD (M)">AHA-Alkyne-KDDDD (M)</option>
       <option value="AHA-SS (M)">AHA-SS (M)</option>
@@ -290,7 +305,9 @@
       <option value="Asp-&gt;Tyr (D)">Asp-&gt;Tyr (D)</option>
       <option value="Asp-&gt;Val (D)">Asp-&gt;Val (D)</option>
       <option value="Asp-&gt;Xle (D)">Asp-&gt;Xle (D)</option>
+      <option value="Aspartylurea (H)">Aspartylurea (H)</option>
       <option value="Atto495Maleimide (C)">Atto495Maleimide (C)</option>
+      <option value="AzidoF (F)">AzidoF (F)</option>
       <option value="azole (C)">azole (C)</option>
       <option value="azole (S)">azole (S)</option>
       <option value="Bacillosamine (N)">Bacillosamine (N)</option>
@@ -300,11 +317,17 @@
       <option value="BDMAPP (Protein N-term)">BDMAPP (Protein N-term)</option>
       <option value="BDMAPP (W)">BDMAPP (W)</option>
       <option value="BDMAPP (Y)">BDMAPP (Y)</option>
+      <option value="BEMAD_C (C)">BEMAD_C (C)</option>
+      <option value="BEMAD_C:2H(6) (C)">BEMAD_C:2H(6) (C)</option>
+      <option value="BEMAD_ST (S)">BEMAD_ST (S)</option>
+      <option value="BEMAD_ST (T)">BEMAD_ST (T)</option>
+      <option value="BEMAD_ST:2H(6) (S)">BEMAD_ST:2H(6) (S)</option>
+      <option value="BEMAD_ST:2H(6) (T)">BEMAD_ST:2H(6) (T)</option>
       <option value="Benzoyl (K)">Benzoyl (K)</option>
       <option value="Benzoyl (N-term)">Benzoyl (N-term)</option>
       <option value="benzylguanidine (K)">benzylguanidine (K)</option>
-      <option value="beta FNA (C)">beta FNA (C)</option>
-      <option value="beta FNA (K)">beta FNA (K)</option>
+      <option value="betaFNA (C)">betaFNA (C)</option>
+      <option value="betaFNA (K)">betaFNA (K)</option>
       <option value="BHT (C)">BHT (C)</option>
       <option value="BHT (H)">BHT (H)</option>
       <option value="BHT (K)">BHT (K)</option>
@@ -327,6 +350,8 @@
       <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
       <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option>
       <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option>
+      <option value="Biotin:Thermo-21328 (K)">Biotin:Thermo-21328 (K)</option>
+      <option value="Biotin:Thermo-21328 (N-term)">Biotin:Thermo-21328 (N-term)</option>
       <option value="Biotin:Thermo-21330 (K)">Biotin:Thermo-21330 (K)</option>
       <option value="Biotin:Thermo-21330 (N-term)">Biotin:Thermo-21330 (N-term)</option>
       <option value="Biotin:Thermo-21345 (Q)">Biotin:Thermo-21345 (Q)</option>
@@ -350,7 +375,6 @@
       <option value="BITC (C)">BITC (C)</option>
       <option value="BITC (K)">BITC (K)</option>
       <option value="BITC (N-term)">BITC (N-term)</option>
-      <option value="BMOE (C)">BMOE (C)</option>
       <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
       <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
       <option value="Bodipy (C)">Bodipy (C)</option>
@@ -375,6 +399,7 @@
       <option value="Carbamidomethyl (E)">Carbamidomethyl (E)</option>
       <option value="Carbamidomethyl (H)">Carbamidomethyl (H)</option>
       <option value="Carbamidomethyl (K)">Carbamidomethyl (K)</option>
+      <option value="Carbamidomethyl (M)">Carbamidomethyl (M)</option>
       <option value="Carbamidomethyl (N-term)">Carbamidomethyl (N-term)</option>
       <option value="Carbamidomethyl (S)">Carbamidomethyl (S)</option>
       <option value="Carbamidomethyl (T)">Carbamidomethyl (T)</option>
@@ -391,6 +416,14 @@
       <option value="Carbamyl (T)">Carbamyl (T)</option>
       <option value="Carbamyl (Y)">Carbamyl (Y)</option>
       <option value="Carbofuran (S)">Carbofuran (S)</option>
+      <option value="Carbonyl (A)">Carbonyl (A)</option>
+      <option value="Carbonyl (E)">Carbonyl (E)</option>
+      <option value="Carbonyl (I)">Carbonyl (I)</option>
+      <option value="Carbonyl (L)">Carbonyl (L)</option>
+      <option value="Carbonyl (Q)">Carbonyl (Q)</option>
+      <option value="Carbonyl (R)">Carbonyl (R)</option>
+      <option value="Carbonyl (S)">Carbonyl (S)</option>
+      <option value="Carbonyl (V)">Carbonyl (V)</option>
       <option value="Carboxy (D)">Carboxy (D)</option>
       <option value="Carboxy (E)">Carboxy (E)</option>
       <option value="Carboxy (K)">Carboxy (K)</option>
@@ -411,6 +444,9 @@
       <option value="Cation:Ag (C-term)">Cation:Ag (C-term)</option>
       <option value="Cation:Ag (D)">Cation:Ag (D)</option>
       <option value="Cation:Ag (E)">Cation:Ag (E)</option>
+      <option value="Cation:Al[III] (C-term)">Cation:Al[III] (C-term)</option>
+      <option value="Cation:Al[III] (D)">Cation:Al[III] (D)</option>
+      <option value="Cation:Al[III] (E)">Cation:Al[III] (E)</option>
       <option value="Cation:Ca[II] (C-term)">Cation:Ca[II] (C-term)</option>
       <option value="Cation:Ca[II] (D)">Cation:Ca[II] (D)</option>
       <option value="Cation:Ca[II] (E)">Cation:Ca[II] (E)</option>
@@ -421,6 +457,9 @@
       <option value="Cation:Fe[II] (C-term)">Cation:Fe[II] (C-term)</option>
       <option value="Cation:Fe[II] (D)">Cation:Fe[II] (D)</option>
       <option value="Cation:Fe[II] (E)">Cation:Fe[II] (E)</option>
+      <option value="Cation:Fe[III] (C-term)">Cation:Fe[III] (C-term)</option>
+      <option value="Cation:Fe[III] (D)">Cation:Fe[III] (D)</option>
+      <option value="Cation:Fe[III] (E)">Cation:Fe[III] (E)</option>
       <option value="Cation:K (C-term)">Cation:K (C-term)</option>
       <option value="Cation:K (D)">Cation:K (D)</option>
       <option value="Cation:K (E)">Cation:K (E)</option>
@@ -445,11 +484,10 @@
       <option value="cGMP+RMP-loss (C)">cGMP+RMP-loss (C)</option>
       <option value="cGMP+RMP-loss (S)">cGMP+RMP-loss (S)</option>
       <option value="CHDH (D)">CHDH (D)</option>
+      <option value="Chlorination (W)">Chlorination (W)</option>
       <option value="Chlorination (Y)">Chlorination (Y)</option>
-      <option value="Chlorpyrifos (S)">Chlorpyrifos (S)</option>
-      <option value="Chlorpyrifos (T)">Chlorpyrifos (T)</option>
-      <option value="Chlorpyrifos (Y)">Chlorpyrifos (Y)</option>
       <option value="Cholesterol (Protein C-term)">Cholesterol (Protein C-term)</option>
+      <option value="CIGG (K)">CIGG (K)</option>
       <option value="CLIP_TRAQ_2 (K)">CLIP_TRAQ_2 (K)</option>
       <option value="CLIP_TRAQ_2 (N-term)">CLIP_TRAQ_2 (N-term)</option>
       <option value="CLIP_TRAQ_2 (Y)">CLIP_TRAQ_2 (Y)</option>
@@ -760,6 +798,8 @@
       <option value="Deamidated:18O(1) (Q)">Deamidated:18O(1) (Q)</option>
       <option value="Decanoyl (S)">Decanoyl (S)</option>
       <option value="Decanoyl (T)">Decanoyl (T)</option>
+      <option value="Decarboxylation (D)">Decarboxylation (D)</option>
+      <option value="Decarboxylation (E)">Decarboxylation (E)</option>
       <option value="DEDGFLYMVYASQETFG (K)">DEDGFLYMVYASQETFG (K)</option>
       <option value="Dehydrated (D)">Dehydrated (D)</option>
       <option value="Dehydrated (N-term C)">Dehydrated (N-term C)</option>
@@ -769,7 +809,10 @@
       <option value="Dehydrated (T)">Dehydrated (T)</option>
       <option value="Dehydrated (Y)">Dehydrated (Y)</option>
       <option value="Dehydro (C)">Dehydro (C)</option>
+      <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
+      <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
       <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
+      <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
       <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
       <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
       <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option>
@@ -778,6 +821,7 @@
       <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
       <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
       <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
+      <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
       <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
       <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
       <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -788,6 +832,8 @@
       <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option>
       <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
       <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
+      <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+      <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
       <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
       <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
       <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option>
@@ -795,10 +841,12 @@
       <option value="Delta:H(6)C(3)O(1) (K)">Delta:H(6)C(3)O(1) (K)</option>
       <option value="Delta:H(6)C(3)O(1) (Protein N-term)">Delta:H(6)C(3)O(1) (Protein N-term)</option>
       <option value="Delta:H(6)C(6)O(1) (K)">Delta:H(6)C(6)O(1) (K)</option>
+      <option value="Delta:H(6)C(7)O(4) (R)">Delta:H(6)C(7)O(4) (R)</option>
       <option value="Delta:H(8)C(6)O(1) (K)">Delta:H(8)C(6)O(1) (K)</option>
       <option value="Delta:H(8)C(6)O(1) (Protein N-term)">Delta:H(8)C(6)O(1) (Protein N-term)</option>
       <option value="Delta:H(8)C(6)O(2) (K)">Delta:H(8)C(6)O(2) (K)</option>
       <option value="Delta:Hg(1) (C)">Delta:Hg(1) (C)</option>
+      <option value="Delta:O(4) (W)">Delta:O(4) (W)</option>
       <option value="Delta:S(-1)Se(1) (C)">Delta:S(-1)Se(1) (C)</option>
       <option value="Delta:S(-1)Se(1) (M)">Delta:S(-1)Se(1) (M)</option>
       <option value="Delta:Se(1) (C)">Delta:Se(1) (C)</option>
@@ -809,10 +857,6 @@
       <option value="Deoxyhypusine (Q)">Deoxyhypusine (Q)</option>
       <option value="DeStreak (C)">DeStreak (C)</option>
       <option value="Dethiomethyl (M)">Dethiomethyl (M)</option>
-      <option value="DFDNB (K)">DFDNB (K)</option>
-      <option value="DFDNB (N)">DFDNB (N)</option>
-      <option value="DFDNB (Q)">DFDNB (Q)</option>
-      <option value="DFDNB (R)">DFDNB (R)</option>
       <option value="dHex (N)">dHex (N)</option>
       <option value="dHex (S)">dHex (S)</option>
       <option value="dHex (T)">dHex (T)</option>
@@ -834,8 +878,6 @@
       <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
       <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S)</option>
       <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuGc(1) (S)">dHex(1)Hex(1)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuGc(1) (T)">dHex(1)Hex(1)HexNAc(2)NeuGc(1) (T)</option>
       <option value="dHex(1)Hex(1)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(2)Sulf(1) (S)</option>
       <option value="dHex(1)Hex(1)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(2)Sulf(1) (T)</option>
       <option value="dHex(1)Hex(1)HexNAc(3) (S)">dHex(1)Hex(1)HexNAc(3) (S)</option>
@@ -862,6 +904,8 @@
       <option value="dHex(1)Hex(2)HexA(1)HexNAc(2) (T)">dHex(1)Hex(2)HexA(1)HexNAc(2) (T)</option>
       <option value="dHex(1)Hex(2)HexNAc(1) (S)">dHex(1)Hex(2)HexNAc(1) (S)</option>
       <option value="dHex(1)Hex(2)HexNAc(1) (T)">dHex(1)Hex(2)HexNAc(1) (T)</option>
+      <option value="dHex(1)Hex(2)HexNAc(1)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(1)NeuAc(2) (S)</option>
+      <option value="dHex(1)Hex(2)HexNAc(1)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(1)NeuAc(2) (T)</option>
       <option value="dHex(1)Hex(2)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(1)Sulf(1) (S)</option>
       <option value="dHex(1)Hex(2)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(1)Sulf(1) (T)</option>
       <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
@@ -870,6 +914,7 @@
       <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T)</option>
       <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
       <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
+      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (N)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (N)</option>
       <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S)</option>
       <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T)</option>
       <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S)</option>
@@ -888,12 +933,15 @@
       <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
       <option value="dHex(1)Hex(2)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(3)Sulf(1) (S)</option>
       <option value="dHex(1)Hex(2)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(3)Sulf(1) (T)</option>
+      <option value="dHex(1)Hex(2)HexNAc(4) (N)">dHex(1)Hex(2)HexNAc(4) (N)</option>
       <option value="dHex(1)Hex(2)HexNAc(4) (S)">dHex(1)Hex(2)HexNAc(4) (S)</option>
       <option value="dHex(1)Hex(2)HexNAc(4) (T)">dHex(1)Hex(2)HexNAc(4) (T)</option>
       <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(1) (S)">dHex(1)Hex(2)HexNAc(4)NeuAc(1) (S)</option>
       <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(1) (T)">dHex(1)Hex(2)HexNAc(4)NeuAc(1) (T)</option>
       <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(4)NeuAc(2) (S)</option>
       <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(4)NeuAc(2) (T)</option>
+      <option value="dHex(1)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(1)Hex(2)HexNAc(4)Sulf(2) (S)</option>
+      <option value="dHex(1)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(1)Hex(2)HexNAc(4)Sulf(2) (T)</option>
       <option value="dHex(1)Hex(3) (S)">dHex(1)Hex(3) (S)</option>
       <option value="dHex(1)Hex(3) (T)">dHex(1)Hex(3) (T)</option>
       <option value="dHex(1)Hex(3)HexA(1)HexNAc(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(1) (S)</option>
@@ -952,6 +1000,8 @@
       <option value="dHex(1)Hex(3)HexNAc(6)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(6)Sulf(1) (N)</option>
       <option value="dHex(1)Hex(4) (S)">dHex(1)Hex(4) (S)</option>
       <option value="dHex(1)Hex(4) (T)">dHex(1)Hex(4) (T)</option>
+      <option value="dHex(1)Hex(4)HexA(1) (S)">dHex(1)Hex(4)HexA(1) (S)</option>
+      <option value="dHex(1)Hex(4)HexA(1) (T)">dHex(1)Hex(4)HexA(1) (T)</option>
       <option value="dHex(1)Hex(4)HexA(1)HexNAc(2) (S)">dHex(1)Hex(4)HexA(1)HexNAc(2) (S)</option>
       <option value="dHex(1)Hex(4)HexA(1)HexNAc(2) (T)">dHex(1)Hex(4)HexA(1)HexNAc(2) (T)</option>
       <option value="dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)</option>
@@ -963,6 +1013,8 @@
       <option value="dHex(1)Hex(4)HexNAc(2)Pent(1) (N)">dHex(1)Hex(4)HexNAc(2)Pent(1) (N)</option>
       <option value="dHex(1)Hex(4)HexNAc(3) (N)">dHex(1)Hex(4)HexNAc(3) (N)</option>
       <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (N)</option>
+      <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (S)</option>
+      <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (T)</option>
       <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
       <option value="dHex(1)Hex(4)HexNAc(3)NeuGc(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuGc(1) (N)</option>
       <option value="dHex(1)Hex(4)HexNAc(3)Pent(1) (N)">dHex(1)Hex(4)HexNAc(3)Pent(1) (N)</option>
@@ -1009,6 +1061,7 @@
       <option value="dHex(1)Hex(7)HexNAc(3)Phos(1) (N)">dHex(1)Hex(7)HexNAc(3)Phos(1) (N)</option>
       <option value="dHex(1)Hex(7)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(7)HexNAc(3)Sulf(1) (N)</option>
       <option value="dHex(1)Hex(7)HexNAc(4) (N)">dHex(1)Hex(7)HexNAc(4) (N)</option>
+      <option value="dHex(1)Hex(8)HexNAc(2) (N)">dHex(1)Hex(8)HexNAc(2) (N)</option>
       <option value="dHex(1)HexNAc(3) (S)">dHex(1)HexNAc(3) (S)</option>
       <option value="dHex(1)HexNAc(3) (T)">dHex(1)HexNAc(3) (T)</option>
       <option value="dHex(1)HexNAc(4) (S)">dHex(1)HexNAc(4) (S)</option>
@@ -1025,6 +1078,8 @@
       <option value="dHex(2)Hex(1)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(1)HexNAc(2)NeuGc(1) (T)</option>
       <option value="dHex(2)Hex(1)HexNAc(3) (S)">dHex(2)Hex(1)HexNAc(3) (S)</option>
       <option value="dHex(2)Hex(1)HexNAc(3) (T)">dHex(2)Hex(1)HexNAc(3) (T)</option>
+      <option value="dHex(2)Hex(1)HexNAc(4)Sulf(1) (S)">dHex(2)Hex(1)HexNAc(4)Sulf(1) (S)</option>
+      <option value="dHex(2)Hex(1)HexNAc(4)Sulf(1) (T)">dHex(2)Hex(1)HexNAc(4)Sulf(1) (T)</option>
       <option value="dHex(2)Hex(2) (S)">dHex(2)Hex(2) (S)</option>
       <option value="dHex(2)Hex(2) (T)">dHex(2)Hex(2) (T)</option>
       <option value="dHex(2)Hex(2)HexA(1) (S)">dHex(2)Hex(2)HexA(1) (S)</option>
@@ -1061,8 +1116,12 @@
       <option value="dHex(2)Hex(2)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(3)Sulf(1) (T)</option>
       <option value="dHex(2)Hex(2)HexNAc(4) (S)">dHex(2)Hex(2)HexNAc(4) (S)</option>
       <option value="dHex(2)Hex(2)HexNAc(4) (T)">dHex(2)Hex(2)HexNAc(4) (T)</option>
+      <option value="dHex(2)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(2)Hex(2)HexNAc(4)Sulf(2) (S)</option>
+      <option value="dHex(2)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(2)Hex(2)HexNAc(4)Sulf(2) (T)</option>
       <option value="dHex(2)Hex(2)HexNAc(5) (S)">dHex(2)Hex(2)HexNAc(5) (S)</option>
       <option value="dHex(2)Hex(2)HexNAc(5) (T)">dHex(2)Hex(2)HexNAc(5) (T)</option>
+      <option value="dHex(2)Hex(2)HexNAc(6)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(6)Sulf(1) (S)</option>
+      <option value="dHex(2)Hex(2)HexNAc(6)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(6)Sulf(1) (T)</option>
       <option value="dHex(2)Hex(3) (S)">dHex(2)Hex(3) (S)</option>
       <option value="dHex(2)Hex(3) (T)">dHex(2)Hex(3) (T)</option>
       <option value="dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)</option>
@@ -1087,15 +1146,17 @@
       <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(1) (T)">dHex(2)Hex(3)HexNAc(3)NeuAc(1) (T)</option>
       <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(2) (S)">dHex(2)Hex(3)HexNAc(3)NeuAc(2) (S)</option>
       <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(2) (T)">dHex(2)Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)NeuGc(1) (S)">dHex(2)Hex(3)HexNAc(3)NeuGc(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)NeuGc(1) (T)">dHex(2)Hex(3)HexNAc(3)NeuGc(1) (T)</option>
       <option value="dHex(2)Hex(3)HexNAc(3)Pent(1) (N)">dHex(2)Hex(3)HexNAc(3)Pent(1) (N)</option>
       <option value="dHex(2)Hex(3)HexNAc(3)Pent(2) (N)">dHex(2)Hex(3)HexNAc(3)Pent(2) (N)</option>
+      <option value="dHex(2)Hex(3)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(3)Sulf(1) (S)</option>
+      <option value="dHex(2)Hex(3)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(3)Sulf(1) (T)</option>
       <option value="dHex(2)Hex(3)HexNAc(4) (N)">dHex(2)Hex(3)HexNAc(4) (N)</option>
       <option value="dHex(2)Hex(3)HexNAc(4) (S)">dHex(2)Hex(3)HexNAc(4) (S)</option>
       <option value="dHex(2)Hex(3)HexNAc(4) (T)">dHex(2)Hex(3)HexNAc(4) (T)</option>
+      <option value="dHex(2)Hex(3)HexNAc(4)NeuAc(1) (N)">dHex(2)Hex(3)HexNAc(4)NeuAc(1) (N)</option>
       <option value="dHex(2)Hex(3)HexNAc(4)Pent(1) (N)">dHex(2)Hex(3)HexNAc(4)Pent(1) (N)</option>
       <option value="dHex(2)Hex(3)HexNAc(4)Pent(2) (N)">dHex(2)Hex(3)HexNAc(4)Pent(2) (N)</option>
+      <option value="dHex(2)Hex(3)HexNAc(5) (N)">dHex(2)Hex(3)HexNAc(5) (N)</option>
       <option value="dHex(2)Hex(3)HexNAc(5) (S)">dHex(2)Hex(3)HexNAc(5) (S)</option>
       <option value="dHex(2)Hex(3)HexNAc(5) (T)">dHex(2)Hex(3)HexNAc(5) (T)</option>
       <option value="dHex(2)Hex(3)HexNAc(6) (N)">dHex(2)Hex(3)HexNAc(6) (N)</option>
@@ -1119,6 +1180,8 @@
       <option value="dHex(2)Hex(4)HexNAc(5) (N)">dHex(2)Hex(4)HexNAc(5) (N)</option>
       <option value="dHex(2)Hex(4)HexNAc(5) (S)">dHex(2)Hex(4)HexNAc(5) (S)</option>
       <option value="dHex(2)Hex(4)HexNAc(5) (T)">dHex(2)Hex(4)HexNAc(5) (T)</option>
+      <option value="dHex(2)Hex(5)HexNAc(2)Me(1) (S)">dHex(2)Hex(5)HexNAc(2)Me(1) (S)</option>
+      <option value="dHex(2)Hex(5)HexNAc(2)Me(1) (T)">dHex(2)Hex(5)HexNAc(2)Me(1) (T)</option>
       <option value="dHex(2)Hex(5)HexNAc(3)Pent(1) (N)">dHex(2)Hex(5)HexNAc(3)Pent(1) (N)</option>
       <option value="dHex(2)Hex(5)HexNAc(4) (N)">dHex(2)Hex(5)HexNAc(4) (N)</option>
       <option value="dHex(2)HexNAc(2)Kdn(1) (S)">dHex(2)HexNAc(2)Kdn(1) (S)</option>
@@ -1143,6 +1206,12 @@
       <option value="dHex(3)Hex(2)HexNAc(3)Kdn(1) (T)">dHex(3)Hex(2)HexNAc(3)Kdn(1) (T)</option>
       <option value="dHex(3)Hex(2)HexNAc(4) (S)">dHex(3)Hex(2)HexNAc(4) (S)</option>
       <option value="dHex(3)Hex(2)HexNAc(4) (T)">dHex(3)Hex(2)HexNAc(4) (T)</option>
+      <option value="dHex(3)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(3)Hex(2)HexNAc(4)Sulf(2) (S)</option>
+      <option value="dHex(3)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(3)Hex(2)HexNAc(4)Sulf(2) (T)</option>
+      <option value="dHex(3)Hex(3)HexNAc(1) (S)">dHex(3)Hex(3)HexNAc(1) (S)</option>
+      <option value="dHex(3)Hex(3)HexNAc(1) (T)">dHex(3)Hex(3)HexNAc(1) (T)</option>
+      <option value="dHex(3)Hex(3)HexNAc(2) (S)">dHex(3)Hex(3)HexNAc(2) (S)</option>
+      <option value="dHex(3)Hex(3)HexNAc(2) (T)">dHex(3)Hex(3)HexNAc(2) (T)</option>
       <option value="dHex(3)Hex(3)HexNAc(3) (S)">dHex(3)Hex(3)HexNAc(3) (S)</option>
       <option value="dHex(3)Hex(3)HexNAc(3) (T)">dHex(3)Hex(3)HexNAc(3) (T)</option>
       <option value="dHex(3)Hex(3)HexNAc(3)NeuAc(1) (S)">dHex(3)Hex(3)HexNAc(3)NeuAc(1) (S)</option>
@@ -1166,6 +1235,8 @@
       <option value="dHex(4)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(4)Hex(2)HexNAc(2)Kdn(1) (T)</option>
       <option value="dHex(4)Hex(2)HexNAc(3) (S)">dHex(4)Hex(2)HexNAc(3) (S)</option>
       <option value="dHex(4)Hex(2)HexNAc(3) (T)">dHex(4)Hex(2)HexNAc(3) (T)</option>
+      <option value="dHex(4)Hex(3)HexNAc(2)NeuAc(1) (S)">dHex(4)Hex(3)HexNAc(2)NeuAc(1) (S)</option>
+      <option value="dHex(4)Hex(3)HexNAc(2)NeuAc(1) (T)">dHex(4)Hex(3)HexNAc(2)NeuAc(1) (T)</option>
       <option value="dHex(4)Hex(3)HexNAc(3) (S)">dHex(4)Hex(3)HexNAc(3) (S)</option>
       <option value="dHex(4)Hex(3)HexNAc(3) (T)">dHex(4)Hex(3)HexNAc(3) (T)</option>
       <option value="dHex(4)HexNAc(3)Kdn(1) (S)">dHex(4)HexNAc(3)Kdn(1) (S)</option>
@@ -1214,6 +1285,12 @@
       <option value="Diethylphosphate (S)">Diethylphosphate (S)</option>
       <option value="Diethylphosphate (T)">Diethylphosphate (T)</option>
       <option value="Diethylphosphate (Y)">Diethylphosphate (Y)</option>
+      <option value="Diethylphosphothione (C)">Diethylphosphothione (C)</option>
+      <option value="Diethylphosphothione (H)">Diethylphosphothione (H)</option>
+      <option value="Diethylphosphothione (K)">Diethylphosphothione (K)</option>
+      <option value="Diethylphosphothione (S)">Diethylphosphothione (S)</option>
+      <option value="Diethylphosphothione (T)">Diethylphosphothione (T)</option>
+      <option value="Diethylphosphothione (Y)">Diethylphosphothione (Y)</option>
       <option value="Difuran (Y)">Difuran (Y)</option>
       <option value="Dihydroxyimidazolidine (R)">Dihydroxyimidazolidine (R)</option>
       <option value="Diiodo (H)">Diiodo (H)</option>
@@ -1263,15 +1340,26 @@
       <option value="Dimethyl:2H(6)13C(2) (Protein N-term)">Dimethyl:2H(6)13C(2) (Protein N-term)</option>
       <option value="Dimethyl:2H(6)13C(2) (R)">Dimethyl:2H(6)13C(2) (R)</option>
       <option value="DimethylamineGMBS (C)">DimethylamineGMBS (C)</option>
+      <option value="Dimethylaminoethyl (C)">Dimethylaminoethyl (C)</option>
       <option value="DimethylArsino (C)">DimethylArsino (C)</option>
+      <option value="Dimethylphosphothione (C)">Dimethylphosphothione (C)</option>
+      <option value="Dimethylphosphothione (H)">Dimethylphosphothione (H)</option>
+      <option value="Dimethylphosphothione (K)">Dimethylphosphothione (K)</option>
+      <option value="Dimethylphosphothione (S)">Dimethylphosphothione (S)</option>
+      <option value="Dimethylphosphothione (T)">Dimethylphosphothione (T)</option>
+      <option value="Dimethylphosphothione (Y)">Dimethylphosphothione (Y)</option>
       <option value="DimethylpyrroleAdduct (K)">DimethylpyrroleAdduct (K)</option>
       <option value="Dioxidation (C)">Dioxidation (C)</option>
+      <option value="Dioxidation (E)">Dioxidation (E)</option>
       <option value="Dioxidation (F)">Dioxidation (F)</option>
+      <option value="Dioxidation (I)">Dioxidation (I)</option>
       <option value="Dioxidation (K)">Dioxidation (K)</option>
+      <option value="Dioxidation (L)">Dioxidation (L)</option>
       <option value="Dioxidation (M)">Dioxidation (M)</option>
       <option value="Dioxidation (P)">Dioxidation (P)</option>
       <option value="Dioxidation (R)">Dioxidation (R)</option>
       <option value="Dioxidation (U)">Dioxidation (U)</option>
+      <option value="Dioxidation (V)">Dioxidation (V)</option>
       <option value="Dioxidation (W)">Dioxidation (W)</option>
       <option value="Dioxidation (Y)">Dioxidation (Y)</option>
       <option value="Diphthamide (H)">Diphthamide (H)</option>
@@ -1288,18 +1376,9 @@
       <option value="dNIC (N-term)">dNIC (N-term)</option>
       <option value="DNPS (C)">DNPS (C)</option>
       <option value="DNPS (W)">DNPS (W)</option>
-      <option value="DTBP (K)">DTBP (K)</option>
-      <option value="DTBP (N)">DTBP (N)</option>
-      <option value="DTBP (Protein N-term)">DTBP (Protein N-term)</option>
-      <option value="DTBP (Q)">DTBP (Q)</option>
-      <option value="DTBP (R)">DTBP (R)</option>
-      <option value="DTT_C (C)">DTT_C (C)</option>
-      <option value="DTT_C:2H(6) (C)">DTT_C:2H(6) (C)</option>
-      <option value="DTT_ST (S)">DTT_ST (S)</option>
-      <option value="DTT_ST (T)">DTT_ST (T)</option>
-      <option value="DTT_ST:2H(6) (S)">DTT_ST:2H(6) (S)</option>
-      <option value="DTT_ST:2H(6) (T)">DTT_ST:2H(6) (T)</option>
+      <option value="DTT (C)">DTT (C)</option>
       <option value="DyLight-maleimide (C)">DyLight-maleimide (C)</option>
+      <option value="DYn-2 (C)">DYn-2 (C)</option>
       <option value="EDEDTIDVFQQQTGG (K)">EDEDTIDVFQQQTGG (K)</option>
       <option value="EDT-iodoacetyl-PEO-biotin (S)">EDT-iodoacetyl-PEO-biotin (S)</option>
       <option value="EDT-iodoacetyl-PEO-biotin (T)">EDT-iodoacetyl-PEO-biotin (T)</option>
@@ -1368,6 +1447,7 @@
       <option value="Formyl (Protein N-term)">Formyl (Protein N-term)</option>
       <option value="Formyl (S)">Formyl (S)</option>
       <option value="Formyl (T)">Formyl (T)</option>
+      <option value="Formylasparagine (H)">Formylasparagine (H)</option>
       <option value="FormylMet (Protein N-term)">FormylMet (Protein N-term)</option>
       <option value="FP-Biotin (K)">FP-Biotin (K)</option>
       <option value="FP-Biotin (S)">FP-Biotin (S)</option>
@@ -1386,6 +1466,7 @@
       <option value="GeranylGeranyl (C)">GeranylGeranyl (C)</option>
       <option value="GG (C)">GG (C)</option>
       <option value="GG (K)">GG (K)</option>
+      <option value="GG (Protein N-term)">GG (Protein N-term)</option>
       <option value="GG (S)">GG (S)</option>
       <option value="GG (T)">GG (T)</option>
       <option value="GGQ (K)">GGQ (K)</option>
@@ -1452,6 +1533,7 @@
       <option value="GluGluGlu (Protein C-term)">GluGluGlu (Protein C-term)</option>
       <option value="GluGluGluGlu (E)">GluGluGluGlu (E)</option>
       <option value="GluGluGluGlu (Protein C-term)">GluGluGluGlu (Protein C-term)</option>
+      <option value="Gluratylation (K)">Gluratylation (K)</option>
       <option value="Glutathione (C)">Glutathione (C)</option>
       <option value="Gly (K)">Gly (K)</option>
       <option value="Gly (S)">Gly (S)</option>
@@ -1480,9 +1562,17 @@
       <option value="glycidamide (K)">glycidamide (K)</option>
       <option value="glycidamide (N-term)">glycidamide (N-term)</option>
       <option value="Glycosyl (P)">Glycosyl (P)</option>
+      <option value="glyoxalAGE (R)">glyoxalAGE (R)</option>
+      <option value="GNLLFLACYCIGG (K)">GNLLFLACYCIGG (K)</option>
       <option value="GPIanchor (Protein C-term)">GPIanchor (Protein C-term)</option>
       <option value="Guanidinyl (K)">Guanidinyl (K)</option>
       <option value="Guanidinyl (N-term)">Guanidinyl (N-term)</option>
+      <option value="Haloxon (C)">Haloxon (C)</option>
+      <option value="Haloxon (H)">Haloxon (H)</option>
+      <option value="Haloxon (K)">Haloxon (K)</option>
+      <option value="Haloxon (S)">Haloxon (S)</option>
+      <option value="Haloxon (T)">Haloxon (T)</option>
+      <option value="Haloxon (Y)">Haloxon (Y)</option>
       <option value="HCysteinyl (C)">HCysteinyl (C)</option>
       <option value="HCysThiolactone (K)">HCysThiolactone (K)</option>
       <option value="Heme (C)">Heme (C)</option>
@@ -1562,6 +1652,8 @@
       <option value="Hex(1)HexNAc(2)dHex(2) (N)">Hex(1)HexNAc(2)dHex(2) (N)</option>
       <option value="Hex(1)HexNAc(2)dHex(2) (S)">Hex(1)HexNAc(2)dHex(2) (S)</option>
       <option value="Hex(1)HexNAc(2)dHex(2) (T)">Hex(1)HexNAc(2)dHex(2) (T)</option>
+      <option value="Hex(1)HexNAc(2)dHex(2)Sulf(1) (S)">Hex(1)HexNAc(2)dHex(2)Sulf(1) (S)</option>
+      <option value="Hex(1)HexNAc(2)dHex(2)Sulf(1) (T)">Hex(1)HexNAc(2)dHex(2)Sulf(1) (T)</option>
       <option value="Hex(1)HexNAc(2)NeuAc(1) (S)">Hex(1)HexNAc(2)NeuAc(1) (S)</option>
       <option value="Hex(1)HexNAc(2)NeuAc(1) (T)">Hex(1)HexNAc(2)NeuAc(1) (T)</option>
       <option value="Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)">Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
@@ -1585,6 +1677,8 @@
       <option value="Hex(1)HexNAc(3)NeuGc(1) (T)">Hex(1)HexNAc(3)NeuGc(1) (T)</option>
       <option value="Hex(1)HexNAc(3)Sulf(1) (S)">Hex(1)HexNAc(3)Sulf(1) (S)</option>
       <option value="Hex(1)HexNAc(3)Sulf(1) (T)">Hex(1)HexNAc(3)Sulf(1) (T)</option>
+      <option value="Hex(1)HexNAc(4)dHex(1)Sulf(1) (S)">Hex(1)HexNAc(4)dHex(1)Sulf(1) (S)</option>
+      <option value="Hex(1)HexNAc(4)dHex(1)Sulf(1) (T)">Hex(1)HexNAc(4)dHex(1)Sulf(1) (T)</option>
       <option value="Hex(1)NeuAc(1) (S)">Hex(1)NeuAc(1) (S)</option>
       <option value="Hex(1)NeuAc(1) (T)">Hex(1)NeuAc(1) (T)</option>
       <option value="Hex(1)NeuAc(1)Pent(1) (S)">Hex(1)NeuAc(1)Pent(1) (S)</option>
@@ -1595,16 +1689,26 @@
       <option value="Hex(1)Pent(1) (T)">Hex(1)Pent(1) (T)</option>
       <option value="Hex(1)Pent(2) (S)">Hex(1)Pent(2) (S)</option>
       <option value="Hex(1)Pent(2) (T)">Hex(1)Pent(2) (T)</option>
+      <option value="Hex(1)Pent(2)Me(1) (S)">Hex(1)Pent(2)Me(1) (S)</option>
+      <option value="Hex(1)Pent(2)Me(1) (T)">Hex(1)Pent(2)Me(1) (T)</option>
+      <option value="Hex(1)Pent(3) (S)">Hex(1)Pent(3) (S)</option>
+      <option value="Hex(1)Pent(3) (T)">Hex(1)Pent(3) (T)</option>
+      <option value="Hex(1)Pent(3)Me(1) (S)">Hex(1)Pent(3)Me(1) (S)</option>
+      <option value="Hex(1)Pent(3)Me(1) (T)">Hex(1)Pent(3)Me(1) (T)</option>
+      <option value="Hex(10)HexNAc(1) (N)">Hex(10)HexNAc(1) (N)</option>
       <option value="Hex(10)Phos(3) (S)">Hex(10)Phos(3) (S)</option>
       <option value="Hex(10)Phos(3) (T)">Hex(10)Phos(3) (T)</option>
       <option value="Hex(2) (K)">Hex(2) (K)</option>
       <option value="Hex(2) (R)">Hex(2) (R)</option>
+      <option value="Hex(2) (S)">Hex(2) (S)</option>
+      <option value="Hex(2) (T)">Hex(2) (T)</option>
       <option value="Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)">Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)</option>
       <option value="Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)">Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)</option>
       <option value="Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S)">Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S)</option>
       <option value="Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T)">Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T)</option>
       <option value="Hex(2)HexA(1)Pent(1)Sulf(1) (S)">Hex(2)HexA(1)Pent(1)Sulf(1) (S)</option>
       <option value="Hex(2)HexA(1)Pent(1)Sulf(1) (T)">Hex(2)HexA(1)Pent(1)Sulf(1) (T)</option>
+      <option value="Hex(2)HexNAc(1) (N)">Hex(2)HexNAc(1) (N)</option>
       <option value="Hex(2)HexNAc(1) (S)">Hex(2)HexNAc(1) (S)</option>
       <option value="Hex(2)HexNAc(1) (T)">Hex(2)HexNAc(1) (T)</option>
       <option value="Hex(2)HexNAc(1)Me(1) (S)">Hex(2)HexNAc(1)Me(1) (S)</option>
@@ -1617,6 +1721,8 @@
       <option value="Hex(2)HexNAc(1)NeuGc(3) (T)">Hex(2)HexNAc(1)NeuGc(3) (T)</option>
       <option value="Hex(2)HexNAc(1)NeuGc(4) (S)">Hex(2)HexNAc(1)NeuGc(4) (S)</option>
       <option value="Hex(2)HexNAc(1)NeuGc(4) (T)">Hex(2)HexNAc(1)NeuGc(4) (T)</option>
+      <option value="Hex(2)HexNAc(1)Pent(1)HexA(1) (S)">Hex(2)HexNAc(1)Pent(1)HexA(1) (S)</option>
+      <option value="Hex(2)HexNAc(1)Pent(1)HexA(1) (T)">Hex(2)HexNAc(1)Pent(1)HexA(1) (T)</option>
       <option value="Hex(2)HexNAc(1)Sulf(1) (S)">Hex(2)HexNAc(1)Sulf(1) (S)</option>
       <option value="Hex(2)HexNAc(1)Sulf(1) (T)">Hex(2)HexNAc(1)Sulf(1) (T)</option>
       <option value="Hex(2)HexNAc(2) (N)">Hex(2)HexNAc(2) (N)</option>
@@ -1626,6 +1732,8 @@
       <option value="Hex(2)HexNAc(2)dHex(1) (S)">Hex(2)HexNAc(2)dHex(1) (S)</option>
       <option value="Hex(2)HexNAc(2)dHex(1) (T)">Hex(2)HexNAc(2)dHex(1) (T)</option>
       <option value="Hex(2)HexNAc(2)NeuAc(1) (N)">Hex(2)HexNAc(2)NeuAc(1) (N)</option>
+      <option value="Hex(2)HexNAc(2)NeuAc(1) (S)">Hex(2)HexNAc(2)NeuAc(1) (S)</option>
+      <option value="Hex(2)HexNAc(2)NeuAc(1) (T)">Hex(2)HexNAc(2)NeuAc(1) (T)</option>
       <option value="Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
       <option value="Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
       <option value="Hex(2)HexNAc(2)NeuAc(2) (S)">Hex(2)HexNAc(2)NeuAc(2) (S)</option>
@@ -1637,6 +1745,7 @@
       <option value="Hex(2)HexNAc(2)Pent(1) (N)">Hex(2)HexNAc(2)Pent(1) (N)</option>
       <option value="Hex(2)HexNAc(2)Sulf(1) (S)">Hex(2)HexNAc(2)Sulf(1) (S)</option>
       <option value="Hex(2)HexNAc(2)Sulf(1) (T)">Hex(2)HexNAc(2)Sulf(1) (T)</option>
+      <option value="Hex(2)HexNAc(3) (N)">Hex(2)HexNAc(3) (N)</option>
       <option value="Hex(2)HexNAc(3) (S)">Hex(2)HexNAc(3) (S)</option>
       <option value="Hex(2)HexNAc(3) (T)">Hex(2)HexNAc(3) (T)</option>
       <option value="Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S)">Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S)</option>
@@ -1655,6 +1764,7 @@
       <option value="Hex(2)HexNAc(3)NeuGc(3) (T)">Hex(2)HexNAc(3)NeuGc(3) (T)</option>
       <option value="Hex(2)HexNAc(3)Sulf(1) (S)">Hex(2)HexNAc(3)Sulf(1) (S)</option>
       <option value="Hex(2)HexNAc(3)Sulf(1) (T)">Hex(2)HexNAc(3)Sulf(1) (T)</option>
+      <option value="Hex(2)HexNAc(4) (N)">Hex(2)HexNAc(4) (N)</option>
       <option value="Hex(2)HexNAc(4) (S)">Hex(2)HexNAc(4) (S)</option>
       <option value="Hex(2)HexNAc(4) (T)">Hex(2)HexNAc(4) (T)</option>
       <option value="Hex(2)HexNAc(4)NeuAc(1) (S)">Hex(2)HexNAc(4)NeuAc(1) (S)</option>
@@ -1663,11 +1773,20 @@
       <option value="Hex(2)HexNAc(5) (T)">Hex(2)HexNAc(5) (T)</option>
       <option value="Hex(2)NeuAc(1) (S)">Hex(2)NeuAc(1) (S)</option>
       <option value="Hex(2)NeuAc(1) (T)">Hex(2)NeuAc(1) (T)</option>
+      <option value="Hex(2)Pent(2) (S)">Hex(2)Pent(2) (S)</option>
+      <option value="Hex(2)Pent(2) (T)">Hex(2)Pent(2) (T)</option>
+      <option value="Hex(2)Pent(2)Me(1) (S)">Hex(2)Pent(2)Me(1) (S)</option>
+      <option value="Hex(2)Pent(2)Me(1) (T)">Hex(2)Pent(2)Me(1) (T)</option>
+      <option value="Hex(2)Sulf(1) (S)">Hex(2)Sulf(1) (S)</option>
+      <option value="Hex(2)Sulf(1) (T)">Hex(2)Sulf(1) (T)</option>
       <option value="Hex(3) (N)">Hex(3) (N)</option>
       <option value="Hex(3) (S)">Hex(3) (S)</option>
       <option value="Hex(3) (T)">Hex(3) (T)</option>
+      <option value="Hex(3)HexNAc(1) (N)">Hex(3)HexNAc(1) (N)</option>
       <option value="Hex(3)HexNAc(1) (S)">Hex(3)HexNAc(1) (S)</option>
       <option value="Hex(3)HexNAc(1) (T)">Hex(3)HexNAc(1) (T)</option>
+      <option value="Hex(3)HexNAc(1)HexA(1) (S)">Hex(3)HexNAc(1)HexA(1) (S)</option>
+      <option value="Hex(3)HexNAc(1)HexA(1) (T)">Hex(3)HexNAc(1)HexA(1) (T)</option>
       <option value="Hex(3)HexNAc(1)Me(1) (S)">Hex(3)HexNAc(1)Me(1) (S)</option>
       <option value="Hex(3)HexNAc(1)Me(1) (T)">Hex(3)HexNAc(1)Me(1) (T)</option>
       <option value="Hex(3)HexNAc(1)Pent(1) (N)">Hex(3)HexNAc(1)Pent(1) (N)</option>
@@ -1690,22 +1809,27 @@
       <option value="Hex(3)HexNAc(3)NeuAc(2) (T)">Hex(3)HexNAc(3)NeuAc(2) (T)</option>
       <option value="Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S)">Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S)</option>
       <option value="Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T)">Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T)</option>
+      <option value="Hex(3)HexNAc(3)NeuAc(3) (S)">Hex(3)HexNAc(3)NeuAc(3) (S)</option>
+      <option value="Hex(3)HexNAc(3)NeuAc(3) (T)">Hex(3)HexNAc(3)NeuAc(3) (T)</option>
       <option value="Hex(3)HexNAc(3)NeuGc(1) (S)">Hex(3)HexNAc(3)NeuGc(1) (S)</option>
       <option value="Hex(3)HexNAc(3)NeuGc(1) (T)">Hex(3)HexNAc(3)NeuGc(1) (T)</option>
       <option value="Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S)">Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S)</option>
       <option value="Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T)">Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T)</option>
       <option value="Hex(3)HexNAc(3)Pent(1) (N)">Hex(3)HexNAc(3)Pent(1) (N)</option>
+      <option value="Hex(3)HexNAc(3)Sulf(1) (N)">Hex(3)HexNAc(3)Sulf(1) (N)</option>
       <option value="Hex(3)HexNAc(3)Sulf(1) (S)">Hex(3)HexNAc(3)Sulf(1) (S)</option>
       <option value="Hex(3)HexNAc(3)Sulf(1) (T)">Hex(3)HexNAc(3)Sulf(1) (T)</option>
       <option value="Hex(3)HexNAc(4) (N)">Hex(3)HexNAc(4) (N)</option>
       <option value="Hex(3)HexNAc(4) (S)">Hex(3)HexNAc(4) (S)</option>
       <option value="Hex(3)HexNAc(4) (T)">Hex(3)HexNAc(4) (T)</option>
       <option value="Hex(3)HexNAc(4)NeuAc(1) (N)">Hex(3)HexNAc(4)NeuAc(1) (N)</option>
+      <option value="Hex(3)HexNAc(4)NeuAc(2) (N)">Hex(3)HexNAc(4)NeuAc(2) (N)</option>
       <option value="Hex(3)HexNAc(4)Pent(1) (N)">Hex(3)HexNAc(4)Pent(1) (N)</option>
       <option value="Hex(3)HexNAc(4)Sulf(1) (N)">Hex(3)HexNAc(4)Sulf(1) (N)</option>
       <option value="Hex(3)HexNAc(5) (N)">Hex(3)HexNAc(5) (N)</option>
       <option value="Hex(3)HexNAc(5) (S)">Hex(3)HexNAc(5) (S)</option>
       <option value="Hex(3)HexNAc(5) (T)">Hex(3)HexNAc(5) (T)</option>
+      <option value="Hex(3)HexNAc(5)NeuAc(1) (N)">Hex(3)HexNAc(5)NeuAc(1) (N)</option>
       <option value="Hex(3)HexNAc(5)Sulf(1) (N)">Hex(3)HexNAc(5)Sulf(1) (N)</option>
       <option value="Hex(3)HexNAc(6) (N)">Hex(3)HexNAc(6) (N)</option>
       <option value="Hex(3)HexNAc(6) (S)">Hex(3)HexNAc(6) (S)</option>
@@ -1715,14 +1839,19 @@
       <option value="Hex(3)HexNAc(6)Sulf(2) (N)">Hex(3)HexNAc(6)Sulf(2) (N)</option>
       <option value="Hex(3)HexNAc(7) (N)">Hex(3)HexNAc(7) (N)</option>
       <option value="Hex(3)HexNAc(7)Sulf(1) (N)">Hex(3)HexNAc(7)Sulf(1) (N)</option>
-      <option value="Hex(3)Phos(1) (S)">Hex(3)Phos(1) (S)</option>
-      <option value="Hex(3)Phos(1) (T)">Hex(3)Phos(1) (T)</option>
       <option value="Hex(4) (S)">Hex(4) (S)</option>
       <option value="Hex(4) (T)">Hex(4) (T)</option>
+      <option value="Hex(4)HexA(1) (S)">Hex(4)HexA(1) (S)</option>
+      <option value="Hex(4)HexA(1) (T)">Hex(4)HexA(1) (T)</option>
+      <option value="Hex(4)HexA(1)HexNAc(1) (S)">Hex(4)HexA(1)HexNAc(1) (S)</option>
+      <option value="Hex(4)HexA(1)HexNAc(1) (T)">Hex(4)HexA(1)HexNAc(1) (T)</option>
+      <option value="Hex(4)HexNAc(1) (N)">Hex(4)HexNAc(1) (N)</option>
       <option value="Hex(4)HexNAc(1) (S)">Hex(4)HexNAc(1) (S)</option>
       <option value="Hex(4)HexNAc(1) (T)">Hex(4)HexNAc(1) (T)</option>
       <option value="Hex(4)HexNAc(2) (N)">Hex(4)HexNAc(2) (N)</option>
       <option value="Hex(4)HexNAc(2)NeuAc(1) (N)">Hex(4)HexNAc(2)NeuAc(1) (N)</option>
+      <option value="Hex(4)HexNAc(2)NeuAc(1) (S)">Hex(4)HexNAc(2)NeuAc(1) (S)</option>
+      <option value="Hex(4)HexNAc(2)NeuAc(1) (T)">Hex(4)HexNAc(2)NeuAc(1) (T)</option>
       <option value="Hex(4)HexNAc(2)Pent(1) (N)">Hex(4)HexNAc(2)Pent(1) (N)</option>
       <option value="Hex(4)HexNAc(3) (N)">Hex(4)HexNAc(3) (N)</option>
       <option value="Hex(4)HexNAc(3) (S)">Hex(4)HexNAc(3) (S)</option>
@@ -1744,6 +1873,9 @@
       <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T)">Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T)</option>
       <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S)">Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S)</option>
       <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T)">Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T)</option>
+      <option value="Hex(4)HexNAc(4)NeuGc(1) (N)">Hex(4)HexNAc(4)NeuGc(1) (N)</option>
+      <option value="Hex(4)HexNAc(4)NeuGc(1) (S)">Hex(4)HexNAc(4)NeuGc(1) (S)</option>
+      <option value="Hex(4)HexNAc(4)NeuGc(1) (T)">Hex(4)HexNAc(4)NeuGc(1) (T)</option>
       <option value="Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S)">Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S)</option>
       <option value="Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T)">Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T)</option>
       <option value="Hex(4)HexNAc(4)Pent(1) (N)">Hex(4)HexNAc(4)Pent(1) (N)</option>
@@ -1758,6 +1890,9 @@
       <option value="Hex(4)Phos(1) (T)">Hex(4)Phos(1) (T)</option>
       <option value="Hex(5) (S)">Hex(5) (S)</option>
       <option value="Hex(5) (T)">Hex(5) (T)</option>
+      <option value="Hex(5)HexA(1) (S)">Hex(5)HexA(1) (S)</option>
+      <option value="Hex(5)HexA(1) (T)">Hex(5)HexA(1) (T)</option>
+      <option value="Hex(5)HexNAc(1) (N)">Hex(5)HexNAc(1) (N)</option>
       <option value="Hex(5)HexNAc(1) (S)">Hex(5)HexNAc(1) (S)</option>
       <option value="Hex(5)HexNAc(1) (T)">Hex(5)HexNAc(1) (T)</option>
       <option value="Hex(5)HexNAc(2) (N)">Hex(5)HexNAc(2) (N)</option>
@@ -1769,6 +1904,8 @@
       <option value="Hex(5)HexNAc(4) (T)">Hex(5)HexNAc(4) (T)</option>
       <option value="Hex(5)HexNAc(4)Me(2)Pent(1) (N)">Hex(5)HexNAc(4)Me(2)Pent(1) (N)</option>
       <option value="Hex(5)HexNAc(4)NeuAc(1) (N)">Hex(5)HexNAc(4)NeuAc(1) (N)</option>
+      <option value="Hex(5)HexNAc(4)NeuAc(1)Ac(1) (N)">Hex(5)HexNAc(4)NeuAc(1)Ac(1) (N)</option>
+      <option value="Hex(5)HexNAc(4)NeuAc(1)Ac(2) (N)">Hex(5)HexNAc(4)NeuAc(1)Ac(2) (N)</option>
       <option value="Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N)">Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N)</option>
       <option value="Hex(5)HexNAc(4)NeuAc(2) (N)">Hex(5)HexNAc(4)NeuAc(2) (N)</option>
       <option value="Hex(5)HexNAc(4)NeuGc(1) (N)">Hex(5)HexNAc(4)NeuGc(1) (N)</option>
@@ -1780,6 +1917,7 @@
       <option value="Hex(5)Phos(1) (T)">Hex(5)Phos(1) (T)</option>
       <option value="Hex(5)Phos(3) (S)">Hex(5)Phos(3) (S)</option>
       <option value="Hex(5)Phos(3) (T)">Hex(5)Phos(3) (T)</option>
+      <option value="Hex(6)HexNAc(1) (N)">Hex(6)HexNAc(1) (N)</option>
       <option value="Hex(6)HexNAc(2) (N)">Hex(6)HexNAc(2) (N)</option>
       <option value="Hex(6)HexNAc(2)Phos(1) (N)">Hex(6)HexNAc(2)Phos(1) (N)</option>
       <option value="Hex(6)HexNAc(3) (N)">Hex(6)HexNAc(3) (N)</option>
@@ -1807,14 +1945,19 @@
       <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option>
       <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option>
       <option value="Hex(8)Phos(3) (T)">Hex(8)Phos(3) (T)</option>
+      <option value="Hex(9) (N)">Hex(9) (N)</option>
+      <option value="Hex(9)HexNAc(1) (N)">Hex(9)HexNAc(1) (N)</option>
       <option value="Hex(9)HexNAc(2) (N)">Hex(9)HexNAc(2) (N)</option>
       <option value="Hex(9)Phos(3) (S)">Hex(9)Phos(3) (S)</option>
       <option value="Hex(9)Phos(3) (T)">Hex(9)Phos(3) (T)</option>
+      <option value="HexA(2)HexNAc(3) (S)">HexA(2)HexNAc(3) (S)</option>
+      <option value="HexA(2)HexNAc(3) (T)">HexA(2)HexNAc(3) (T)</option>
       <option value="HexN (K)">HexN (K)</option>
       <option value="HexN (N)">HexN (N)</option>
       <option value="HexN (S)">HexN (S)</option>
       <option value="HexN (T)">HexN (T)</option>
       <option value="HexN (W)">HexN (W)</option>
+      <option value="HexNAc (C)">HexNAc (C)</option>
       <option value="HexNAc (N)">HexNAc (N)</option>
       <option value="HexNAc (S)">HexNAc (S)</option>
       <option value="HexNAc (T)">HexNAc (T)</option>
@@ -1841,6 +1984,8 @@
       <option value="HexNAc(2)NeuAc(1)Sulf(1) (T)">HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
       <option value="HexNAc(2)NeuGc(1) (S)">HexNAc(2)NeuGc(1) (S)</option>
       <option value="HexNAc(2)NeuGc(1) (T)">HexNAc(2)NeuGc(1) (T)</option>
+      <option value="HexNAc(2)Sulf(1) (S)">HexNAc(2)Sulf(1) (S)</option>
+      <option value="HexNAc(2)Sulf(1) (T)">HexNAc(2)Sulf(1) (T)</option>
       <option value="HexNAc(3) (S)">HexNAc(3) (S)</option>
       <option value="HexNAc(3) (T)">HexNAc(3) (T)</option>
       <option value="HexNAc(3)Sulf(1) (S)">HexNAc(3)Sulf(1) (S)</option>
@@ -1895,6 +2040,7 @@
       <option value="Hydroxycinnamyl (C)">Hydroxycinnamyl (C)</option>
       <option value="Hydroxyfarnesyl (C)">Hydroxyfarnesyl (C)</option>
       <option value="Hydroxyheme (E)">Hydroxyheme (E)</option>
+      <option value="hydroxyisobutyryl (K)">hydroxyisobutyryl (K)</option>
       <option value="Hydroxymethyl (N)">Hydroxymethyl (N)</option>
       <option value="HydroxymethylOP (K)">HydroxymethylOP (K)</option>
       <option value="Hydroxytrimethyl (K)">Hydroxytrimethyl (K)</option>
@@ -1957,6 +2103,7 @@
       <option value="Isopropylphospho (S)">Isopropylphospho (S)</option>
       <option value="Isopropylphospho (T)">Isopropylphospho (T)</option>
       <option value="Isopropylphospho (Y)">Isopropylphospho (Y)</option>
+      <option value="iTRAQ4plex (C)">iTRAQ4plex (C)</option>
       <option value="iTRAQ4plex (H)">iTRAQ4plex (H)</option>
       <option value="iTRAQ4plex (K)">iTRAQ4plex (K)</option>
       <option value="iTRAQ4plex (N-term)">iTRAQ4plex (N-term)</option>
@@ -1964,12 +2111,15 @@
       <option value="iTRAQ4plex (S)">iTRAQ4plex (S)</option>
       <option value="iTRAQ4plex (T)">iTRAQ4plex (T)</option>
       <option value="iTRAQ4plex (Y)">iTRAQ4plex (Y)</option>
+      <option value="iTRAQ4plex114 (C)">iTRAQ4plex114 (C)</option>
       <option value="iTRAQ4plex114 (K)">iTRAQ4plex114 (K)</option>
       <option value="iTRAQ4plex114 (N-term)">iTRAQ4plex114 (N-term)</option>
       <option value="iTRAQ4plex114 (Y)">iTRAQ4plex114 (Y)</option>
+      <option value="iTRAQ4plex115 (C)">iTRAQ4plex115 (C)</option>
       <option value="iTRAQ4plex115 (K)">iTRAQ4plex115 (K)</option>
       <option value="iTRAQ4plex115 (N-term)">iTRAQ4plex115 (N-term)</option>
       <option value="iTRAQ4plex115 (Y)">iTRAQ4plex115 (Y)</option>
+      <option value="iTRAQ8plex (C)">iTRAQ8plex (C)</option>
       <option value="iTRAQ8plex (H)">iTRAQ8plex (H)</option>
       <option value="iTRAQ8plex (K)">iTRAQ8plex (K)</option>
       <option value="iTRAQ8plex (N-term)">iTRAQ8plex (N-term)</option>
@@ -1977,6 +2127,7 @@
       <option value="iTRAQ8plex (S)">iTRAQ8plex (S)</option>
       <option value="iTRAQ8plex (T)">iTRAQ8plex (T)</option>
       <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option>
+      <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
@@ -2046,8 +2197,10 @@
       <option value="Label:2H(3) (L)">Label:2H(3) (L)</option>
       <option value="Label:2H(3) (M)">Label:2H(3) (M)</option>
       <option value="Label:2H(3)+Oxidation (M)">Label:2H(3)+Oxidation (M)</option>
+      <option value="Label:2H(4) (A)">Label:2H(4) (A)</option>
       <option value="Label:2H(4) (F)">Label:2H(4) (F)</option>
       <option value="Label:2H(4) (K)">Label:2H(4) (K)</option>
+      <option value="Label:2H(4) (U)">Label:2H(4) (U)</option>
       <option value="Label:2H(4) (Y)">Label:2H(4) (Y)</option>
       <option value="Label:2H(4)+Acetyl (K)">Label:2H(4)+Acetyl (K)</option>
       <option value="Label:2H(4)+GG (K)">Label:2H(4)+GG (K)</option>
@@ -2106,19 +2259,25 @@
       <option value="maleimide5 (C)">maleimide5 (C)</option>
       <option value="maleimide5 (K)">maleimide5 (K)</option>
       <option value="Malonyl (C)">Malonyl (C)</option>
+      <option value="Malonyl (K)">Malonyl (K)</option>
       <option value="Malonyl (S)">Malonyl (S)</option>
       <option value="MDCC (C)">MDCC (C)</option>
+      <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
       <option value="Menadione (C)">Menadione (C)</option>
       <option value="Menadione (K)">Menadione (K)</option>
       <option value="Menadione-HQ (C)">Menadione-HQ (C)</option>
       <option value="Menadione-HQ (K)">Menadione-HQ (K)</option>
       <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option>
       <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option>
+      <option value="MesitylOxide (H)">MesitylOxide (H)</option>
+      <option value="MesitylOxide (K)">MesitylOxide (K)</option>
+      <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
       <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
       <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
       <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
       <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option>
       <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option>
+      <option value="Met-&gt;AspSA (M)">Met-&gt;AspSA (M)</option>
       <option value="Met-&gt;Cys (M)">Met-&gt;Cys (M)</option>
       <option value="Met-&gt;Gln (M)">Met-&gt;Gln (M)</option>
       <option value="Met-&gt;Glu (M)">Met-&gt;Glu (M)</option>
@@ -2138,6 +2297,18 @@
       <option value="Met-&gt;Xle (M)">Met-&gt;Xle (M)</option>
       <option value="Met-loss (Protein N-term M)">Met-loss (Protein N-term M)</option>
       <option value="Met-loss+Acetyl (Protein N-term M)">Met-loss+Acetyl (Protein N-term M)</option>
+      <option value="Methamidophos-O (C)">Methamidophos-O (C)</option>
+      <option value="Methamidophos-O (H)">Methamidophos-O (H)</option>
+      <option value="Methamidophos-O (K)">Methamidophos-O (K)</option>
+      <option value="Methamidophos-O (S)">Methamidophos-O (S)</option>
+      <option value="Methamidophos-O (T)">Methamidophos-O (T)</option>
+      <option value="Methamidophos-O (Y)">Methamidophos-O (Y)</option>
+      <option value="Methamidophos-S (C)">Methamidophos-S (C)</option>
+      <option value="Methamidophos-S (H)">Methamidophos-S (H)</option>
+      <option value="Methamidophos-S (K)">Methamidophos-S (K)</option>
+      <option value="Methamidophos-S (S)">Methamidophos-S (S)</option>
+      <option value="Methamidophos-S (T)">Methamidophos-S (T)</option>
+      <option value="Methamidophos-S (Y)">Methamidophos-S (Y)</option>
       <option value="Methyl (C)">Methyl (C)</option>
       <option value="Methyl (C-term)">Methyl (C-term)</option>
       <option value="Methyl (D)">Methyl (D)</option>
@@ -2186,6 +2357,9 @@
       <option value="Methylamine (S)">Methylamine (S)</option>
       <option value="Methylamine (T)">Methylamine (T)</option>
       <option value="Methylmalonylation (S)">Methylmalonylation (S)</option>
+      <option value="methylol (K)">methylol (K)</option>
+      <option value="methylol (W)">methylol (W)</option>
+      <option value="methylol (Y)">methylol (Y)</option>
       <option value="Methylphosphonate (S)">Methylphosphonate (S)</option>
       <option value="Methylphosphonate (T)">Methylphosphonate (T)</option>
       <option value="Methylphosphonate (Y)">Methylphosphonate (Y)</option>
@@ -2207,6 +2381,12 @@
       <option value="MolybdopterinGD (D)">MolybdopterinGD (D)</option>
       <option value="MolybdopterinGD (U)">MolybdopterinGD (U)</option>
       <option value="MolybdopterinGD+Delta:S(-1)Se(1) (C)">MolybdopterinGD+Delta:S(-1)Se(1) (C)</option>
+      <option value="monomethylphosphothione (C)">monomethylphosphothione (C)</option>
+      <option value="monomethylphosphothione (H)">monomethylphosphothione (H)</option>
+      <option value="monomethylphosphothione (K)">monomethylphosphothione (K)</option>
+      <option value="monomethylphosphothione (S)">monomethylphosphothione (S)</option>
+      <option value="monomethylphosphothione (T)">monomethylphosphothione (T)</option>
+      <option value="monomethylphosphothione (Y)">monomethylphosphothione (Y)</option>
       <option value="mTRAQ (H)">mTRAQ (H)</option>
       <option value="mTRAQ (K)">mTRAQ (K)</option>
       <option value="mTRAQ (N-term)">mTRAQ (N-term)</option>
@@ -2264,9 +2444,12 @@
       <option value="NIC (K)">NIC (K)</option>
       <option value="NIC (N-term)">NIC (N-term)</option>
       <option value="NIPCAM (C)">NIPCAM (C)</option>
+      <option value="Nitrene (Y)">Nitrene (Y)</option>
+      <option value="Nitro (F)">Nitro (F)</option>
       <option value="Nitro (W)">Nitro (W)</option>
       <option value="Nitro (Y)">Nitro (Y)</option>
       <option value="Nitrosyl (C)">Nitrosyl (C)</option>
+      <option value="Nitrosyl (Y)">Nitrosyl (Y)</option>
       <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option>
       <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option>
       <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
@@ -2298,14 +2481,21 @@
       <option value="Oxidation (C)">Oxidation (C)</option>
       <option value="Oxidation (C-term G)">Oxidation (C-term G)</option>
       <option value="Oxidation (D)">Oxidation (D)</option>
+      <option value="Oxidation (E)">Oxidation (E)</option>
       <option value="Oxidation (F)">Oxidation (F)</option>
       <option value="Oxidation (H)">Oxidation (H)</option>
+      <option value="Oxidation (I)">Oxidation (I)</option>
       <option value="Oxidation (K)">Oxidation (K)</option>
+      <option value="Oxidation (L)">Oxidation (L)</option>
       <option value="Oxidation (M)">Oxidation (M)</option>
       <option value="Oxidation (N)">Oxidation (N)</option>
       <option value="Oxidation (P)">Oxidation (P)</option>
+      <option value="Oxidation (Q)">Oxidation (Q)</option>
       <option value="Oxidation (R)">Oxidation (R)</option>
+      <option value="Oxidation (S)">Oxidation (S)</option>
+      <option value="Oxidation (T)">Oxidation (T)</option>
       <option value="Oxidation (U)">Oxidation (U)</option>
+      <option value="Oxidation (V)">Oxidation (V)</option>
       <option value="Oxidation (W)">Oxidation (W)</option>
       <option value="Oxidation (Y)">Oxidation (Y)</option>
       <option value="Oxidation+NEM (C)">Oxidation+NEM (C)</option>
@@ -2324,6 +2514,10 @@
       <option value="PEITC (C)">PEITC (C)</option>
       <option value="PEITC (K)">PEITC (K)</option>
       <option value="PEITC (N-term)">PEITC (N-term)</option>
+      <option value="Pent(1)HexNAc(1) (S)">Pent(1)HexNAc(1) (S)</option>
+      <option value="Pent(1)HexNAc(1) (T)">Pent(1)HexNAc(1) (T)</option>
+      <option value="Pent(2) (S)">Pent(2) (S)</option>
+      <option value="Pent(2) (T)">Pent(2) (T)</option>
       <option value="Pentose (S)">Pentose (S)</option>
       <option value="Pentose (T)">Pentose (T)</option>
       <option value="Pentylamine (Q)">Pentylamine (Q)</option>
@@ -2354,6 +2548,7 @@
       <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
       <option value="Phospho (C)">Phospho (C)</option>
       <option value="Phospho (D)">Phospho (D)</option>
+      <option value="Phospho (E)">Phospho (E)</option>
       <option value="Phospho (H)">Phospho (H)</option>
       <option value="Phospho (K)">Phospho (K)</option>
       <option value="Phospho (R)">Phospho (R)</option>
@@ -2364,6 +2559,9 @@
       <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
       <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
       <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
+      <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
+      <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option>
+      <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option>
       <option value="Phosphogluconoylation (K)">Phosphogluconoylation (K)</option>
       <option value="Phosphogluconoylation (N-term)">Phosphogluconoylation (N-term)</option>
       <option value="Phosphoguanosine (H)">Phosphoguanosine (H)</option>
@@ -2398,6 +2596,7 @@
       <option value="Pro-&gt;Gln (P)">Pro-&gt;Gln (P)</option>
       <option value="Pro-&gt;Glu (P)">Pro-&gt;Glu (P)</option>
       <option value="Pro-&gt;Gly (P)">Pro-&gt;Gly (P)</option>
+      <option value="Pro-&gt;HAVA (P)">Pro-&gt;HAVA (P)</option>
       <option value="Pro-&gt;His (P)">Pro-&gt;His (P)</option>
       <option value="Pro-&gt;Lys (P)">Pro-&gt;Lys (P)</option>
       <option value="Pro-&gt;Met (P)">Pro-&gt;Met (P)</option>
@@ -2501,9 +2700,12 @@
       <option value="Ser-&gt;Tyr (S)">Ser-&gt;Tyr (S)</option>
       <option value="Ser-&gt;Val (S)">Ser-&gt;Val (S)</option>
       <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option>
+      <option value="serotonylation (Q)">serotonylation (Q)</option>
+      <option value="shTMT (K)">shTMT (K)</option>
+      <option value="shTMT (N-term)">shTMT (N-term)</option>
+      <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
       <option value="SMA (K)">SMA (K)</option>
       <option value="SMA (N-term)">SMA (N-term)</option>
-      <option value="SMCC-maleimide (C)">SMCC-maleimide (C)</option>
       <option value="spermidine (Q)">spermidine (Q)</option>
       <option value="spermine (Q)">spermine (Q)</option>
       <option value="SPITC (K)">SPITC (K)</option>
@@ -2540,9 +2742,14 @@
       <option value="TAMRA-FP (S)">TAMRA-FP (S)</option>
       <option value="TAMRA-FP (Y)">TAMRA-FP (Y)</option>
       <option value="Thiadiazole (C)">Thiadiazole (C)</option>
-      <option value="Thiazolidine (N-term C)">Thiazolidine (N-term C)</option>
-      <option value="Thioacyl (K)">Thioacyl (K)</option>
-      <option value="Thioacyl (X)">Thioacyl (X)</option>
+      <option value="Thiazolidine (C)">Thiazolidine (C)</option>
+      <option value="Thiazolidine (F)">Thiazolidine (F)</option>
+      <option value="Thiazolidine (H)">Thiazolidine (H)</option>
+      <option value="Thiazolidine (K)">Thiazolidine (K)</option>
+      <option value="Thiazolidine (Protein N-term)">Thiazolidine (Protein N-term)</option>
+      <option value="Thiazolidine (R)">Thiazolidine (R)</option>
+      <option value="Thiazolidine (W)">Thiazolidine (W)</option>
+      <option value="Thiazolidine (Y)">Thiazolidine (Y)</option>
       <option value="thioacylPA (K)">thioacylPA (K)</option>
       <option value="Thiophos-S-S-biotin (S)">Thiophos-S-S-biotin (S)</option>
       <option value="Thiophos-S-S-biotin (T)">Thiophos-S-S-biotin (T)</option>
@@ -2574,7 +2781,12 @@
       <option value="TMAB (N-term)">TMAB (N-term)</option>
       <option value="TMAB:2H(9) (K)">TMAB:2H(9) (K)</option>
       <option value="TMAB:2H(9) (N-term)">TMAB:2H(9) (N-term)</option>
+      <option value="TMPP-Ac (K)">TMPP-Ac (K)</option>
       <option value="TMPP-Ac (N-term)">TMPP-Ac (N-term)</option>
+      <option value="TMPP-Ac (Y)">TMPP-Ac (Y)</option>
+      <option value="TMPP-Ac:13C(9) (K)">TMPP-Ac:13C(9) (K)</option>
+      <option value="TMPP-Ac:13C(9) (N-term)">TMPP-Ac:13C(9) (N-term)</option>
+      <option value="TMPP-Ac:13C(9) (Y)">TMPP-Ac:13C(9) (Y)</option>
       <option value="TMT (H)">TMT (H)</option>
       <option value="TMT (K)">TMT (K)</option>
       <option value="TMT (N-term)">TMT (N-term)</option>
@@ -2593,6 +2805,18 @@
       <option value="TMT6plex (Protein N-term)">TMT6plex (Protein N-term)</option>
       <option value="TMT6plex (S)">TMT6plex (S)</option>
       <option value="TMT6plex (T)">TMT6plex (T)</option>
+      <option value="TMTpro (H)">TMTpro (H)</option>
+      <option value="TMTpro (K)">TMTpro (K)</option>
+      <option value="TMTpro (N-term)">TMTpro (N-term)</option>
+      <option value="TMTpro (Protein N-term)">TMTpro (Protein N-term)</option>
+      <option value="TMTpro (S)">TMTpro (S)</option>
+      <option value="TMTpro (T)">TMTpro (T)</option>
+      <option value="TMTpro_zero (H)">TMTpro_zero (H)</option>
+      <option value="TMTpro_zero (K)">TMTpro_zero (K)</option>
+      <option value="TMTpro_zero (N-term)">TMTpro_zero (N-term)</option>
+      <option value="TMTpro_zero (Protein N-term)">TMTpro_zero (Protein N-term)</option>
+      <option value="TMTpro_zero (S)">TMTpro_zero (S)</option>
+      <option value="TMTpro_zero (T)">TMTpro_zero (T)</option>
       <option value="TNBS (K)">TNBS (K)</option>
       <option value="TNBS (N-term)">TNBS (N-term)</option>
       <option value="trifluoro (L)">trifluoro (L)</option>
@@ -2606,6 +2830,7 @@
       <option value="Trimethyl:2H(9) (K)">Trimethyl:2H(9) (K)</option>
       <option value="Trimethyl:2H(9) (R)">Trimethyl:2H(9) (R)</option>
       <option value="Trioxidation (C)">Trioxidation (C)</option>
+      <option value="Trioxidation (F)">Trioxidation (F)</option>
       <option value="Trioxidation (W)">Trioxidation (W)</option>
       <option value="Trioxidation (Y)">Trioxidation (Y)</option>
       <option value="Tripalmitate (Protein N-term C)">Tripalmitate (Protein N-term C)</option>
@@ -2664,6 +2889,44 @@
       <option value="UgiJoullieProGly (E)">UgiJoullieProGly (E)</option>
       <option value="UgiJoullieProGlyProGly (D)">UgiJoullieProGlyProGly (D)</option>
       <option value="UgiJoullieProGlyProGly (E)">UgiJoullieProGlyProGly (E)</option>
+      <option value="Unknown:162 (C-term)">Unknown:162 (C-term)</option>
+      <option value="Unknown:162 (D)">Unknown:162 (D)</option>
+      <option value="Unknown:162 (E)">Unknown:162 (E)</option>
+      <option value="Unknown:162 (N-term)">Unknown:162 (N-term)</option>
+      <option value="Unknown:177 (C-term)">Unknown:177 (C-term)</option>
+      <option value="Unknown:177 (D)">Unknown:177 (D)</option>
+      <option value="Unknown:177 (E)">Unknown:177 (E)</option>
+      <option value="Unknown:177 (N-term)">Unknown:177 (N-term)</option>
+      <option value="Unknown:210 (C-term)">Unknown:210 (C-term)</option>
+      <option value="Unknown:210 (D)">Unknown:210 (D)</option>
+      <option value="Unknown:210 (E)">Unknown:210 (E)</option>
+      <option value="Unknown:210 (N-term)">Unknown:210 (N-term)</option>
+      <option value="Unknown:216 (C-term)">Unknown:216 (C-term)</option>
+      <option value="Unknown:216 (D)">Unknown:216 (D)</option>
+      <option value="Unknown:216 (E)">Unknown:216 (E)</option>
+      <option value="Unknown:216 (N-term)">Unknown:216 (N-term)</option>
+      <option value="Unknown:234 (C-term)">Unknown:234 (C-term)</option>
+      <option value="Unknown:234 (D)">Unknown:234 (D)</option>
+      <option value="Unknown:234 (E)">Unknown:234 (E)</option>
+      <option value="Unknown:234 (N-term)">Unknown:234 (N-term)</option>
+      <option value="Unknown:248 (C-term)">Unknown:248 (C-term)</option>
+      <option value="Unknown:248 (D)">Unknown:248 (D)</option>
+      <option value="Unknown:248 (E)">Unknown:248 (E)</option>
+      <option value="Unknown:248 (N-term)">Unknown:248 (N-term)</option>
+      <option value="Unknown:250 (C-term)">Unknown:250 (C-term)</option>
+      <option value="Unknown:250 (D)">Unknown:250 (D)</option>
+      <option value="Unknown:250 (E)">Unknown:250 (E)</option>
+      <option value="Unknown:250 (N-term)">Unknown:250 (N-term)</option>
+      <option value="Unknown:302 (C-term)">Unknown:302 (C-term)</option>
+      <option value="Unknown:302 (D)">Unknown:302 (D)</option>
+      <option value="Unknown:302 (E)">Unknown:302 (E)</option>
+      <option value="Unknown:302 (N-term)">Unknown:302 (N-term)</option>
+      <option value="Unknown:306 (C-term)">Unknown:306 (C-term)</option>
+      <option value="Unknown:306 (D)">Unknown:306 (D)</option>
+      <option value="Unknown:306 (E)">Unknown:306 (E)</option>
+      <option value="Unknown:306 (N-term)">Unknown:306 (N-term)</option>
+      <option value="Unknown:420 (C-term)">Unknown:420 (C-term)</option>
+      <option value="Unknown:420 (N-term)">Unknown:420 (N-term)</option>
       <option value="Val-&gt;Ala (V)">Val-&gt;Ala (V)</option>
       <option value="Val-&gt;Arg (V)">Val-&gt;Arg (V)</option>
       <option value="Val-&gt;Asn (V)">Val-&gt;Asn (V)</option>
@@ -2722,28 +2985,93 @@
       <option value="Xle-&gt;Val (I)">Xle-&gt;Val (I)</option>
       <option value="Xle-&gt;Val (L)">Xle-&gt;Val (L)</option>
       <option value="Xlink:B10621 (C)">Xlink:B10621 (C)</option>
-      <option value="Xlink:DMP (K)">Xlink:DMP (K)</option>
-      <option value="Xlink:DMP (Protein N-term)">Xlink:DMP (Protein N-term)</option>
-      <option value="Xlink:DMP-de (K)">Xlink:DMP-de (K)</option>
-      <option value="Xlink:DMP-de (Protein N-term)">Xlink:DMP-de (Protein N-term)</option>
-      <option value="Xlink:DMP-s (K)">Xlink:DMP-s (K)</option>
-      <option value="Xlink:DMP-s (Protein N-term)">Xlink:DMP-s (Protein N-term)</option>
-      <option value="Xlink:DSS (K)">Xlink:DSS (K)</option>
-      <option value="Xlink:DSS (Protein N-term)">Xlink:DSS (Protein N-term)</option>
-      <option value="Xlink:DSS-NH2 (K)">Xlink:DSS-NH2 (K)</option>
-      <option value="Xlink:DSS-NH2 (Protein N-term)">Xlink:DSS-NH2 (Protein N-term)</option>
-      <option value="Xlink:DST (K)">Xlink:DST (K)</option>
-      <option value="Xlink:DST (Protein N-term)">Xlink:DST (Protein N-term)</option>
-      <option value="Xlink:DTSSP (K)">Xlink:DTSSP (K)</option>
-      <option value="Xlink:DTSSP (Protein N-term)">Xlink:DTSSP (Protein N-term)</option>
-      <option value="Xlink:EGS (K)">Xlink:EGS (K)</option>
-      <option value="Xlink:EGS (Protein N-term)">Xlink:EGS (Protein N-term)</option>
-      <option value="Xlink:EGScleaved (K)">Xlink:EGScleaved (K)</option>
-      <option value="Xlink:EGScleaved (Protein N-term)">Xlink:EGScleaved (Protein N-term)</option>
-      <option value="Xlink:SMCC (C)">Xlink:SMCC (C)</option>
-      <option value="Xlink:SSD (K)">Xlink:SSD (K)</option>
+      <option value="Xlink:BMOE (C)">Xlink:BMOE (C)</option>
+      <option value="Xlink:BS2G[113] (K)">Xlink:BS2G[113] (K)</option>
+      <option value="Xlink:BS2G[113] (Protein N-term)">Xlink:BS2G[113] (Protein N-term)</option>
+      <option value="Xlink:BS2G[114] (K)">Xlink:BS2G[114] (K)</option>
+      <option value="Xlink:BS2G[114] (Protein N-term)">Xlink:BS2G[114] (Protein N-term)</option>
+      <option value="Xlink:BS2G[217] (K)">Xlink:BS2G[217] (K)</option>
+      <option value="Xlink:BS2G[217] (Protein N-term)">Xlink:BS2G[217] (Protein N-term)</option>
+      <option value="Xlink:BS2G[96] (K)">Xlink:BS2G[96] (K)</option>
+      <option value="Xlink:BS2G[96] (Protein N-term)">Xlink:BS2G[96] (Protein N-term)</option>
+      <option value="Xlink:BuUrBu[111] (K)">Xlink:BuUrBu[111] (K)</option>
+      <option value="Xlink:BuUrBu[111] (Protein N-term)">Xlink:BuUrBu[111] (Protein N-term)</option>
+      <option value="Xlink:BuUrBu[196] (K)">Xlink:BuUrBu[196] (K)</option>
+      <option value="Xlink:BuUrBu[196] (Protein N-term)">Xlink:BuUrBu[196] (Protein N-term)</option>
+      <option value="Xlink:BuUrBu[213] (K)">Xlink:BuUrBu[213] (K)</option>
+      <option value="Xlink:BuUrBu[213] (Protein N-term)">Xlink:BuUrBu[213] (Protein N-term)</option>
+      <option value="Xlink:BuUrBu[214] (K)">Xlink:BuUrBu[214] (K)</option>
+      <option value="Xlink:BuUrBu[214] (Protein N-term)">Xlink:BuUrBu[214] (Protein N-term)</option>
+      <option value="Xlink:BuUrBu[317] (K)">Xlink:BuUrBu[317] (K)</option>
+      <option value="Xlink:BuUrBu[317] (Protein N-term)">Xlink:BuUrBu[317] (Protein N-term)</option>
+      <option value="Xlink:BuUrBu[85] (K)">Xlink:BuUrBu[85] (K)</option>
+      <option value="Xlink:BuUrBu[85] (Protein N-term)">Xlink:BuUrBu[85] (Protein N-term)</option>
+      <option value="Xlink:DFDNB (K)">Xlink:DFDNB (K)</option>
+      <option value="Xlink:DFDNB (N)">Xlink:DFDNB (N)</option>
+      <option value="Xlink:DFDNB (Q)">Xlink:DFDNB (Q)</option>
+      <option value="Xlink:DFDNB (R)">Xlink:DFDNB (R)</option>
+      <option value="Xlink:DMP[122] (K)">Xlink:DMP[122] (K)</option>
+      <option value="Xlink:DMP[122] (Protein N-term)">Xlink:DMP[122] (Protein N-term)</option>
+      <option value="Xlink:DMP[139] (K)">Xlink:DMP[139] (K)</option>
+      <option value="Xlink:DMP[139] (Protein N-term)">Xlink:DMP[139] (Protein N-term)</option>
+      <option value="Xlink:DMP[140] (K)">Xlink:DMP[140] (K)</option>
+      <option value="Xlink:DMP[140] (Protein N-term)">Xlink:DMP[140] (Protein N-term)</option>
+      <option value="Xlink:DMP[154] (K)">Xlink:DMP[154] (K)</option>
+      <option value="Xlink:DMP[154] (Protein N-term)">Xlink:DMP[154] (Protein N-term)</option>
+      <option value="Xlink:DSS[138] (K)">Xlink:DSS[138] (K)</option>
+      <option value="Xlink:DSS[138] (Protein N-term)">Xlink:DSS[138] (Protein N-term)</option>
+      <option value="Xlink:DSS[155] (K)">Xlink:DSS[155] (K)</option>
+      <option value="Xlink:DSS[155] (Protein N-term)">Xlink:DSS[155] (Protein N-term)</option>
+      <option value="Xlink:DSS[156] (K)">Xlink:DSS[156] (K)</option>
+      <option value="Xlink:DSS[156] (Protein N-term)">Xlink:DSS[156] (Protein N-term)</option>
+      <option value="Xlink:DSS[259] (K)">Xlink:DSS[259] (K)</option>
+      <option value="Xlink:DSS[259] (Protein N-term)">Xlink:DSS[259] (Protein N-term)</option>
+      <option value="Xlink:DSSO[104] (K)">Xlink:DSSO[104] (K)</option>
+      <option value="Xlink:DSSO[104] (Protein N-term)">Xlink:DSSO[104] (Protein N-term)</option>
+      <option value="Xlink:DSSO[158] (K)">Xlink:DSSO[158] (K)</option>
+      <option value="Xlink:DSSO[158] (Protein N-term)">Xlink:DSSO[158] (Protein N-term)</option>
+      <option value="Xlink:DSSO[175] (K)">Xlink:DSSO[175] (K)</option>
+      <option value="Xlink:DSSO[175] (Protein N-term)">Xlink:DSSO[175] (Protein N-term)</option>
+      <option value="Xlink:DSSO[176] (K)">Xlink:DSSO[176] (K)</option>
+      <option value="Xlink:DSSO[176] (Protein N-term)">Xlink:DSSO[176] (Protein N-term)</option>
+      <option value="Xlink:DSSO[279] (K)">Xlink:DSSO[279] (K)</option>
+      <option value="Xlink:DSSO[279] (Protein N-term)">Xlink:DSSO[279] (Protein N-term)</option>
+      <option value="Xlink:DSSO[54] (K)">Xlink:DSSO[54] (K)</option>
+      <option value="Xlink:DSSO[54] (Protein N-term)">Xlink:DSSO[54] (Protein N-term)</option>
+      <option value="Xlink:DSSO[86] (K)">Xlink:DSSO[86] (K)</option>
+      <option value="Xlink:DSSO[86] (Protein N-term)">Xlink:DSSO[86] (Protein N-term)</option>
+      <option value="Xlink:DST[114] (K)">Xlink:DST[114] (K)</option>
+      <option value="Xlink:DST[114] (Protein N-term)">Xlink:DST[114] (Protein N-term)</option>
+      <option value="Xlink:DST[132] (K)">Xlink:DST[132] (K)</option>
+      <option value="Xlink:DST[132] (Protein N-term)">Xlink:DST[132] (Protein N-term)</option>
+      <option value="Xlink:DST[56] (K)">Xlink:DST[56] (K)</option>
+      <option value="Xlink:DST[56] (Protein N-term)">Xlink:DST[56] (Protein N-term)</option>
+      <option value="Xlink:DTBP[172] (K)">Xlink:DTBP[172] (K)</option>
+      <option value="Xlink:DTBP[172] (Protein N-term)">Xlink:DTBP[172] (Protein N-term)</option>
+      <option value="Xlink:DTBP[87] (K)">Xlink:DTBP[87] (K)</option>
+      <option value="Xlink:DTBP[87] (Protein N-term)">Xlink:DTBP[87] (Protein N-term)</option>
+      <option value="Xlink:DTSSP[174] (K)">Xlink:DTSSP[174] (K)</option>
+      <option value="Xlink:DTSSP[174] (Protein N-term)">Xlink:DTSSP[174] (Protein N-term)</option>
+      <option value="Xlink:DTSSP[192] (K)">Xlink:DTSSP[192] (K)</option>
+      <option value="Xlink:DTSSP[192] (Protein N-term)">Xlink:DTSSP[192] (Protein N-term)</option>
+      <option value="Xlink:DTSSP[88] (K)">Xlink:DTSSP[88] (K)</option>
+      <option value="Xlink:DTSSP[88] (Protein N-term)">Xlink:DTSSP[88] (Protein N-term)</option>
+      <option value="Xlink:EGS[115] (K)">Xlink:EGS[115] (K)</option>
+      <option value="Xlink:EGS[115] (Protein N-term)">Xlink:EGS[115] (Protein N-term)</option>
+      <option value="Xlink:EGS[226] (K)">Xlink:EGS[226] (K)</option>
+      <option value="Xlink:EGS[226] (Protein N-term)">Xlink:EGS[226] (Protein N-term)</option>
+      <option value="Xlink:EGS[244] (K)">Xlink:EGS[244] (K)</option>
+      <option value="Xlink:EGS[244] (Protein N-term)">Xlink:EGS[244] (Protein N-term)</option>
+      <option value="Xlink:SMCC[219] (C)">Xlink:SMCC[219] (C)</option>
+      <option value="Xlink:SMCC[219] (K)">Xlink:SMCC[219] (K)</option>
+      <option value="Xlink:SMCC[219] (Protein N-term)">Xlink:SMCC[219] (Protein N-term)</option>
+      <option value="Xlink:SMCC[237] (C)">Xlink:SMCC[237] (C)</option>
+      <option value="Xlink:SMCC[237] (K)">Xlink:SMCC[237] (K)</option>
+      <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
+      <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
       <option value="ZGB (K)">ZGB (K)</option>
       <option value="ZGB (N-term)">ZGB (N-term)</option>
+      <option value="ZQG (K)">ZQG (K)</option>
       <expand macro="list_string_san"/>
     </param>
     <param name="variable_modifications" argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
@@ -2773,6 +3101,7 @@
       <option value="Acetyl (K)">Acetyl (K)</option>
       <option value="Acetyl (N-term)">Acetyl (N-term)</option>
       <option value="Acetyl (Protein N-term)">Acetyl (Protein N-term)</option>
+      <option value="Acetyl (R)">Acetyl (R)</option>
       <option value="Acetyl (S)">Acetyl (S)</option>
       <option value="Acetyl (T)">Acetyl (T)</option>
       <option value="Acetyl (Y)">Acetyl (Y)</option>
@@ -2804,6 +3133,7 @@
       <option value="AEC-MAEC (T)">AEC-MAEC (T)</option>
       <option value="AEC-MAEC:2H(4) (S)">AEC-MAEC:2H(4) (S)</option>
       <option value="AEC-MAEC:2H(4) (T)">AEC-MAEC:2H(4) (T)</option>
+      <option value="AFB1_Dialdehyde (K)">AFB1_Dialdehyde (K)</option>
       <option value="AHA-Alkyne (M)">AHA-Alkyne (M)</option>
       <option value="AHA-Alkyne-KDDDD (M)">AHA-Alkyne-KDDDD (M)</option>
       <option value="AHA-SS (M)">AHA-SS (M)</option>
@@ -2906,7 +3236,9 @@
       <option value="Asp-&gt;Tyr (D)">Asp-&gt;Tyr (D)</option>
       <option value="Asp-&gt;Val (D)">Asp-&gt;Val (D)</option>
       <option value="Asp-&gt;Xle (D)">Asp-&gt;Xle (D)</option>
+      <option value="Aspartylurea (H)">Aspartylurea (H)</option>
       <option value="Atto495Maleimide (C)">Atto495Maleimide (C)</option>
+      <option value="AzidoF (F)">AzidoF (F)</option>
       <option value="azole (C)">azole (C)</option>
       <option value="azole (S)">azole (S)</option>
       <option value="Bacillosamine (N)">Bacillosamine (N)</option>
@@ -2916,11 +3248,17 @@
       <option value="BDMAPP (Protein N-term)">BDMAPP (Protein N-term)</option>
       <option value="BDMAPP (W)">BDMAPP (W)</option>
       <option value="BDMAPP (Y)">BDMAPP (Y)</option>
+      <option value="BEMAD_C (C)">BEMAD_C (C)</option>
+      <option value="BEMAD_C:2H(6) (C)">BEMAD_C:2H(6) (C)</option>
+      <option value="BEMAD_ST (S)">BEMAD_ST (S)</option>
+      <option value="BEMAD_ST (T)">BEMAD_ST (T)</option>
+      <option value="BEMAD_ST:2H(6) (S)">BEMAD_ST:2H(6) (S)</option>
+      <option value="BEMAD_ST:2H(6) (T)">BEMAD_ST:2H(6) (T)</option>
       <option value="Benzoyl (K)">Benzoyl (K)</option>
       <option value="Benzoyl (N-term)">Benzoyl (N-term)</option>
       <option value="benzylguanidine (K)">benzylguanidine (K)</option>
-      <option value="beta FNA (C)">beta FNA (C)</option>
-      <option value="beta FNA (K)">beta FNA (K)</option>
+      <option value="betaFNA (C)">betaFNA (C)</option>
+      <option value="betaFNA (K)">betaFNA (K)</option>
       <option value="BHT (C)">BHT (C)</option>
       <option value="BHT (H)">BHT (H)</option>
       <option value="BHT (K)">BHT (K)</option>
@@ -2943,6 +3281,8 @@
       <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
       <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option>
       <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option>
+      <option value="Biotin:Thermo-21328 (K)">Biotin:Thermo-21328 (K)</option>
+      <option value="Biotin:Thermo-21328 (N-term)">Biotin:Thermo-21328 (N-term)</option>
       <option value="Biotin:Thermo-21330 (K)">Biotin:Thermo-21330 (K)</option>
       <option value="Biotin:Thermo-21330 (N-term)">Biotin:Thermo-21330 (N-term)</option>
       <option value="Biotin:Thermo-21345 (Q)">Biotin:Thermo-21345 (Q)</option>
@@ -2966,7 +3306,6 @@
       <option value="BITC (C)">BITC (C)</option>
       <option value="BITC (K)">BITC (K)</option>
       <option value="BITC (N-term)">BITC (N-term)</option>
-      <option value="BMOE (C)">BMOE (C)</option>
       <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
       <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
       <option value="Bodipy (C)">Bodipy (C)</option>
@@ -2991,6 +3330,7 @@
       <option value="Carbamidomethyl (E)">Carbamidomethyl (E)</option>
       <option value="Carbamidomethyl (H)">Carbamidomethyl (H)</option>
       <option value="Carbamidomethyl (K)">Carbamidomethyl (K)</option>
+      <option value="Carbamidomethyl (M)">Carbamidomethyl (M)</option>
       <option value="Carbamidomethyl (N-term)">Carbamidomethyl (N-term)</option>
       <option value="Carbamidomethyl (S)">Carbamidomethyl (S)</option>
       <option value="Carbamidomethyl (T)">Carbamidomethyl (T)</option>
@@ -3007,6 +3347,14 @@
       <option value="Carbamyl (T)">Carbamyl (T)</option>
       <option value="Carbamyl (Y)">Carbamyl (Y)</option>
       <option value="Carbofuran (S)">Carbofuran (S)</option>
+      <option value="Carbonyl (A)">Carbonyl (A)</option>
+      <option value="Carbonyl (E)">Carbonyl (E)</option>
+      <option value="Carbonyl (I)">Carbonyl (I)</option>
+      <option value="Carbonyl (L)">Carbonyl (L)</option>
+      <option value="Carbonyl (Q)">Carbonyl (Q)</option>
+      <option value="Carbonyl (R)">Carbonyl (R)</option>
+      <option value="Carbonyl (S)">Carbonyl (S)</option>
+      <option value="Carbonyl (V)">Carbonyl (V)</option>
       <option value="Carboxy (D)">Carboxy (D)</option>
       <option value="Carboxy (E)">Carboxy (E)</option>
       <option value="Carboxy (K)">Carboxy (K)</option>
@@ -3027,6 +3375,9 @@
       <option value="Cation:Ag (C-term)">Cation:Ag (C-term)</option>
       <option value="Cation:Ag (D)">Cation:Ag (D)</option>
       <option value="Cation:Ag (E)">Cation:Ag (E)</option>
+      <option value="Cation:Al[III] (C-term)">Cation:Al[III] (C-term)</option>
+      <option value="Cation:Al[III] (D)">Cation:Al[III] (D)</option>
+      <option value="Cation:Al[III] (E)">Cation:Al[III] (E)</option>
       <option value="Cation:Ca[II] (C-term)">Cation:Ca[II] (C-term)</option>
       <option value="Cation:Ca[II] (D)">Cation:Ca[II] (D)</option>
       <option value="Cation:Ca[II] (E)">Cation:Ca[II] (E)</option>
@@ -3037,6 +3388,9 @@
       <option value="Cation:Fe[II] (C-term)">Cation:Fe[II] (C-term)</option>
       <option value="Cation:Fe[II] (D)">Cation:Fe[II] (D)</option>
       <option value="Cation:Fe[II] (E)">Cation:Fe[II] (E)</option>
+      <option value="Cation:Fe[III] (C-term)">Cation:Fe[III] (C-term)</option>
+      <option value="Cation:Fe[III] (D)">Cation:Fe[III] (D)</option>
+      <option value="Cation:Fe[III] (E)">Cation:Fe[III] (E)</option>
       <option value="Cation:K (C-term)">Cation:K (C-term)</option>
       <option value="Cation:K (D)">Cation:K (D)</option>
       <option value="Cation:K (E)">Cation:K (E)</option>
@@ -3061,11 +3415,10 @@
       <option value="cGMP+RMP-loss (C)">cGMP+RMP-loss (C)</option>
       <option value="cGMP+RMP-loss (S)">cGMP+RMP-loss (S)</option>
       <option value="CHDH (D)">CHDH (D)</option>
+      <option value="Chlorination (W)">Chlorination (W)</option>
       <option value="Chlorination (Y)">Chlorination (Y)</option>
-      <option value="Chlorpyrifos (S)">Chlorpyrifos (S)</option>
-      <option value="Chlorpyrifos (T)">Chlorpyrifos (T)</option>
-      <option value="Chlorpyrifos (Y)">Chlorpyrifos (Y)</option>
       <option value="Cholesterol (Protein C-term)">Cholesterol (Protein C-term)</option>
+      <option value="CIGG (K)">CIGG (K)</option>
       <option value="CLIP_TRAQ_2 (K)">CLIP_TRAQ_2 (K)</option>
       <option value="CLIP_TRAQ_2 (N-term)">CLIP_TRAQ_2 (N-term)</option>
       <option value="CLIP_TRAQ_2 (Y)">CLIP_TRAQ_2 (Y)</option>
@@ -3376,6 +3729,8 @@
       <option value="Deamidated:18O(1) (Q)">Deamidated:18O(1) (Q)</option>
       <option value="Decanoyl (S)">Decanoyl (S)</option>
       <option value="Decanoyl (T)">Decanoyl (T)</option>
+      <option value="Decarboxylation (D)">Decarboxylation (D)</option>
+      <option value="Decarboxylation (E)">Decarboxylation (E)</option>
       <option value="DEDGFLYMVYASQETFG (K)">DEDGFLYMVYASQETFG (K)</option>
       <option value="Dehydrated (D)">Dehydrated (D)</option>
       <option value="Dehydrated (N-term C)">Dehydrated (N-term C)</option>
@@ -3385,7 +3740,10 @@
       <option value="Dehydrated (T)">Dehydrated (T)</option>
       <option value="Dehydrated (Y)">Dehydrated (Y)</option>
       <option value="Dehydro (C)">Dehydro (C)</option>
+      <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
+      <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
       <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
+      <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
       <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
       <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
       <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option>
@@ -3394,6 +3752,7 @@
       <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
       <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
       <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
+      <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
       <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
       <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
       <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -3404,6 +3763,8 @@
       <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option>
       <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
       <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
+      <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+      <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
       <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
       <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
       <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option>
@@ -3411,10 +3772,12 @@
       <option value="Delta:H(6)C(3)O(1) (K)">Delta:H(6)C(3)O(1) (K)</option>
       <option value="Delta:H(6)C(3)O(1) (Protein N-term)">Delta:H(6)C(3)O(1) (Protein N-term)</option>
       <option value="Delta:H(6)C(6)O(1) (K)">Delta:H(6)C(6)O(1) (K)</option>
+      <option value="Delta:H(6)C(7)O(4) (R)">Delta:H(6)C(7)O(4) (R)</option>
       <option value="Delta:H(8)C(6)O(1) (K)">Delta:H(8)C(6)O(1) (K)</option>
       <option value="Delta:H(8)C(6)O(1) (Protein N-term)">Delta:H(8)C(6)O(1) (Protein N-term)</option>
       <option value="Delta:H(8)C(6)O(2) (K)">Delta:H(8)C(6)O(2) (K)</option>
       <option value="Delta:Hg(1) (C)">Delta:Hg(1) (C)</option>
+      <option value="Delta:O(4) (W)">Delta:O(4) (W)</option>
       <option value="Delta:S(-1)Se(1) (C)">Delta:S(-1)Se(1) (C)</option>
       <option value="Delta:S(-1)Se(1) (M)">Delta:S(-1)Se(1) (M)</option>
       <option value="Delta:Se(1) (C)">Delta:Se(1) (C)</option>
@@ -3425,10 +3788,6 @@
       <option value="Deoxyhypusine (Q)">Deoxyhypusine (Q)</option>
       <option value="DeStreak (C)">DeStreak (C)</option>
       <option value="Dethiomethyl (M)">Dethiomethyl (M)</option>
-      <option value="DFDNB (K)">DFDNB (K)</option>
-      <option value="DFDNB (N)">DFDNB (N)</option>
-      <option value="DFDNB (Q)">DFDNB (Q)</option>
-      <option value="DFDNB (R)">DFDNB (R)</option>
       <option value="dHex (N)">dHex (N)</option>
       <option value="dHex (S)">dHex (S)</option>
       <option value="dHex (T)">dHex (T)</option>
@@ -3450,8 +3809,6 @@
       <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
       <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S)</option>
       <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuGc(1) (S)">dHex(1)Hex(1)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuGc(1) (T)">dHex(1)Hex(1)HexNAc(2)NeuGc(1) (T)</option>
       <option value="dHex(1)Hex(1)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(2)Sulf(1) (S)</option>
       <option value="dHex(1)Hex(1)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(2)Sulf(1) (T)</option>
       <option value="dHex(1)Hex(1)HexNAc(3) (S)">dHex(1)Hex(1)HexNAc(3) (S)</option>
@@ -3478,6 +3835,8 @@
       <option value="dHex(1)Hex(2)HexA(1)HexNAc(2) (T)">dHex(1)Hex(2)HexA(1)HexNAc(2) (T)</option>
       <option value="dHex(1)Hex(2)HexNAc(1) (S)">dHex(1)Hex(2)HexNAc(1) (S)</option>
       <option value="dHex(1)Hex(2)HexNAc(1) (T)">dHex(1)Hex(2)HexNAc(1) (T)</option>
+      <option value="dHex(1)Hex(2)HexNAc(1)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(1)NeuAc(2) (S)</option>
+      <option value="dHex(1)Hex(2)HexNAc(1)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(1)NeuAc(2) (T)</option>
       <option value="dHex(1)Hex(2)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(1)Sulf(1) (S)</option>
       <option value="dHex(1)Hex(2)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(1)Sulf(1) (T)</option>
       <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
@@ -3486,6 +3845,7 @@
       <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T)</option>
       <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
       <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
+      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (N)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (N)</option>
       <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S)</option>
       <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T)</option>
       <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S)</option>
@@ -3504,12 +3864,15 @@
       <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
       <option value="dHex(1)Hex(2)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(3)Sulf(1) (S)</option>
       <option value="dHex(1)Hex(2)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(3)Sulf(1) (T)</option>
+      <option value="dHex(1)Hex(2)HexNAc(4) (N)">dHex(1)Hex(2)HexNAc(4) (N)</option>
       <option value="dHex(1)Hex(2)HexNAc(4) (S)">dHex(1)Hex(2)HexNAc(4) (S)</option>
       <option value="dHex(1)Hex(2)HexNAc(4) (T)">dHex(1)Hex(2)HexNAc(4) (T)</option>
       <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(1) (S)">dHex(1)Hex(2)HexNAc(4)NeuAc(1) (S)</option>
       <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(1) (T)">dHex(1)Hex(2)HexNAc(4)NeuAc(1) (T)</option>
       <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(4)NeuAc(2) (S)</option>
       <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(4)NeuAc(2) (T)</option>
+      <option value="dHex(1)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(1)Hex(2)HexNAc(4)Sulf(2) (S)</option>
+      <option value="dHex(1)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(1)Hex(2)HexNAc(4)Sulf(2) (T)</option>
       <option value="dHex(1)Hex(3) (S)">dHex(1)Hex(3) (S)</option>
       <option value="dHex(1)Hex(3) (T)">dHex(1)Hex(3) (T)</option>
       <option value="dHex(1)Hex(3)HexA(1)HexNAc(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(1) (S)</option>
@@ -3568,6 +3931,8 @@
       <option value="dHex(1)Hex(3)HexNAc(6)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(6)Sulf(1) (N)</option>
       <option value="dHex(1)Hex(4) (S)">dHex(1)Hex(4) (S)</option>
       <option value="dHex(1)Hex(4) (T)">dHex(1)Hex(4) (T)</option>
+      <option value="dHex(1)Hex(4)HexA(1) (S)">dHex(1)Hex(4)HexA(1) (S)</option>
+      <option value="dHex(1)Hex(4)HexA(1) (T)">dHex(1)Hex(4)HexA(1) (T)</option>
       <option value="dHex(1)Hex(4)HexA(1)HexNAc(2) (S)">dHex(1)Hex(4)HexA(1)HexNAc(2) (S)</option>
       <option value="dHex(1)Hex(4)HexA(1)HexNAc(2) (T)">dHex(1)Hex(4)HexA(1)HexNAc(2) (T)</option>
       <option value="dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)</option>
@@ -3579,6 +3944,8 @@
       <option value="dHex(1)Hex(4)HexNAc(2)Pent(1) (N)">dHex(1)Hex(4)HexNAc(2)Pent(1) (N)</option>
       <option value="dHex(1)Hex(4)HexNAc(3) (N)">dHex(1)Hex(4)HexNAc(3) (N)</option>
       <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (N)</option>
+      <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (S)</option>
+      <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (T)</option>
       <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
       <option value="dHex(1)Hex(4)HexNAc(3)NeuGc(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuGc(1) (N)</option>
       <option value="dHex(1)Hex(4)HexNAc(3)Pent(1) (N)">dHex(1)Hex(4)HexNAc(3)Pent(1) (N)</option>
@@ -3625,6 +3992,7 @@
       <option value="dHex(1)Hex(7)HexNAc(3)Phos(1) (N)">dHex(1)Hex(7)HexNAc(3)Phos(1) (N)</option>
       <option value="dHex(1)Hex(7)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(7)HexNAc(3)Sulf(1) (N)</option>
       <option value="dHex(1)Hex(7)HexNAc(4) (N)">dHex(1)Hex(7)HexNAc(4) (N)</option>
+      <option value="dHex(1)Hex(8)HexNAc(2) (N)">dHex(1)Hex(8)HexNAc(2) (N)</option>
       <option value="dHex(1)HexNAc(3) (S)">dHex(1)HexNAc(3) (S)</option>
       <option value="dHex(1)HexNAc(3) (T)">dHex(1)HexNAc(3) (T)</option>
       <option value="dHex(1)HexNAc(4) (S)">dHex(1)HexNAc(4) (S)</option>
@@ -3641,6 +4009,8 @@
       <option value="dHex(2)Hex(1)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(1)HexNAc(2)NeuGc(1) (T)</option>
       <option value="dHex(2)Hex(1)HexNAc(3) (S)">dHex(2)Hex(1)HexNAc(3) (S)</option>
       <option value="dHex(2)Hex(1)HexNAc(3) (T)">dHex(2)Hex(1)HexNAc(3) (T)</option>
+      <option value="dHex(2)Hex(1)HexNAc(4)Sulf(1) (S)">dHex(2)Hex(1)HexNAc(4)Sulf(1) (S)</option>
+      <option value="dHex(2)Hex(1)HexNAc(4)Sulf(1) (T)">dHex(2)Hex(1)HexNAc(4)Sulf(1) (T)</option>
       <option value="dHex(2)Hex(2) (S)">dHex(2)Hex(2) (S)</option>
       <option value="dHex(2)Hex(2) (T)">dHex(2)Hex(2) (T)</option>
       <option value="dHex(2)Hex(2)HexA(1) (S)">dHex(2)Hex(2)HexA(1) (S)</option>
@@ -3677,8 +4047,12 @@
       <option value="dHex(2)Hex(2)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(3)Sulf(1) (T)</option>
       <option value="dHex(2)Hex(2)HexNAc(4) (S)">dHex(2)Hex(2)HexNAc(4) (S)</option>
       <option value="dHex(2)Hex(2)HexNAc(4) (T)">dHex(2)Hex(2)HexNAc(4) (T)</option>
+      <option value="dHex(2)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(2)Hex(2)HexNAc(4)Sulf(2) (S)</option>
+      <option value="dHex(2)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(2)Hex(2)HexNAc(4)Sulf(2) (T)</option>
       <option value="dHex(2)Hex(2)HexNAc(5) (S)">dHex(2)Hex(2)HexNAc(5) (S)</option>
       <option value="dHex(2)Hex(2)HexNAc(5) (T)">dHex(2)Hex(2)HexNAc(5) (T)</option>
+      <option value="dHex(2)Hex(2)HexNAc(6)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(6)Sulf(1) (S)</option>
+      <option value="dHex(2)Hex(2)HexNAc(6)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(6)Sulf(1) (T)</option>
       <option value="dHex(2)Hex(3) (S)">dHex(2)Hex(3) (S)</option>
       <option value="dHex(2)Hex(3) (T)">dHex(2)Hex(3) (T)</option>
       <option value="dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)</option>
@@ -3703,15 +4077,17 @@
       <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(1) (T)">dHex(2)Hex(3)HexNAc(3)NeuAc(1) (T)</option>
       <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(2) (S)">dHex(2)Hex(3)HexNAc(3)NeuAc(2) (S)</option>
       <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(2) (T)">dHex(2)Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)NeuGc(1) (S)">dHex(2)Hex(3)HexNAc(3)NeuGc(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)NeuGc(1) (T)">dHex(2)Hex(3)HexNAc(3)NeuGc(1) (T)</option>
       <option value="dHex(2)Hex(3)HexNAc(3)Pent(1) (N)">dHex(2)Hex(3)HexNAc(3)Pent(1) (N)</option>
       <option value="dHex(2)Hex(3)HexNAc(3)Pent(2) (N)">dHex(2)Hex(3)HexNAc(3)Pent(2) (N)</option>
+      <option value="dHex(2)Hex(3)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(3)Sulf(1) (S)</option>
+      <option value="dHex(2)Hex(3)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(3)Sulf(1) (T)</option>
       <option value="dHex(2)Hex(3)HexNAc(4) (N)">dHex(2)Hex(3)HexNAc(4) (N)</option>
       <option value="dHex(2)Hex(3)HexNAc(4) (S)">dHex(2)Hex(3)HexNAc(4) (S)</option>
       <option value="dHex(2)Hex(3)HexNAc(4) (T)">dHex(2)Hex(3)HexNAc(4) (T)</option>
+      <option value="dHex(2)Hex(3)HexNAc(4)NeuAc(1) (N)">dHex(2)Hex(3)HexNAc(4)NeuAc(1) (N)</option>
       <option value="dHex(2)Hex(3)HexNAc(4)Pent(1) (N)">dHex(2)Hex(3)HexNAc(4)Pent(1) (N)</option>
       <option value="dHex(2)Hex(3)HexNAc(4)Pent(2) (N)">dHex(2)Hex(3)HexNAc(4)Pent(2) (N)</option>
+      <option value="dHex(2)Hex(3)HexNAc(5) (N)">dHex(2)Hex(3)HexNAc(5) (N)</option>
       <option value="dHex(2)Hex(3)HexNAc(5) (S)">dHex(2)Hex(3)HexNAc(5) (S)</option>
       <option value="dHex(2)Hex(3)HexNAc(5) (T)">dHex(2)Hex(3)HexNAc(5) (T)</option>
       <option value="dHex(2)Hex(3)HexNAc(6) (N)">dHex(2)Hex(3)HexNAc(6) (N)</option>
@@ -3735,6 +4111,8 @@
       <option value="dHex(2)Hex(4)HexNAc(5) (N)">dHex(2)Hex(4)HexNAc(5) (N)</option>
       <option value="dHex(2)Hex(4)HexNAc(5) (S)">dHex(2)Hex(4)HexNAc(5) (S)</option>
       <option value="dHex(2)Hex(4)HexNAc(5) (T)">dHex(2)Hex(4)HexNAc(5) (T)</option>
+      <option value="dHex(2)Hex(5)HexNAc(2)Me(1) (S)">dHex(2)Hex(5)HexNAc(2)Me(1) (S)</option>
+      <option value="dHex(2)Hex(5)HexNAc(2)Me(1) (T)">dHex(2)Hex(5)HexNAc(2)Me(1) (T)</option>
       <option value="dHex(2)Hex(5)HexNAc(3)Pent(1) (N)">dHex(2)Hex(5)HexNAc(3)Pent(1) (N)</option>
       <option value="dHex(2)Hex(5)HexNAc(4) (N)">dHex(2)Hex(5)HexNAc(4) (N)</option>
       <option value="dHex(2)HexNAc(2)Kdn(1) (S)">dHex(2)HexNAc(2)Kdn(1) (S)</option>
@@ -3759,6 +4137,12 @@
       <option value="dHex(3)Hex(2)HexNAc(3)Kdn(1) (T)">dHex(3)Hex(2)HexNAc(3)Kdn(1) (T)</option>
       <option value="dHex(3)Hex(2)HexNAc(4) (S)">dHex(3)Hex(2)HexNAc(4) (S)</option>
       <option value="dHex(3)Hex(2)HexNAc(4) (T)">dHex(3)Hex(2)HexNAc(4) (T)</option>
+      <option value="dHex(3)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(3)Hex(2)HexNAc(4)Sulf(2) (S)</option>
+      <option value="dHex(3)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(3)Hex(2)HexNAc(4)Sulf(2) (T)</option>
+      <option value="dHex(3)Hex(3)HexNAc(1) (S)">dHex(3)Hex(3)HexNAc(1) (S)</option>
+      <option value="dHex(3)Hex(3)HexNAc(1) (T)">dHex(3)Hex(3)HexNAc(1) (T)</option>
+      <option value="dHex(3)Hex(3)HexNAc(2) (S)">dHex(3)Hex(3)HexNAc(2) (S)</option>
+      <option value="dHex(3)Hex(3)HexNAc(2) (T)">dHex(3)Hex(3)HexNAc(2) (T)</option>
       <option value="dHex(3)Hex(3)HexNAc(3) (S)">dHex(3)Hex(3)HexNAc(3) (S)</option>
       <option value="dHex(3)Hex(3)HexNAc(3) (T)">dHex(3)Hex(3)HexNAc(3) (T)</option>
       <option value="dHex(3)Hex(3)HexNAc(3)NeuAc(1) (S)">dHex(3)Hex(3)HexNAc(3)NeuAc(1) (S)</option>
@@ -3782,6 +4166,8 @@
       <option value="dHex(4)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(4)Hex(2)HexNAc(2)Kdn(1) (T)</option>
       <option value="dHex(4)Hex(2)HexNAc(3) (S)">dHex(4)Hex(2)HexNAc(3) (S)</option>
       <option value="dHex(4)Hex(2)HexNAc(3) (T)">dHex(4)Hex(2)HexNAc(3) (T)</option>
+      <option value="dHex(4)Hex(3)HexNAc(2)NeuAc(1) (S)">dHex(4)Hex(3)HexNAc(2)NeuAc(1) (S)</option>
+      <option value="dHex(4)Hex(3)HexNAc(2)NeuAc(1) (T)">dHex(4)Hex(3)HexNAc(2)NeuAc(1) (T)</option>
       <option value="dHex(4)Hex(3)HexNAc(3) (S)">dHex(4)Hex(3)HexNAc(3) (S)</option>
       <option value="dHex(4)Hex(3)HexNAc(3) (T)">dHex(4)Hex(3)HexNAc(3) (T)</option>
       <option value="dHex(4)HexNAc(3)Kdn(1) (S)">dHex(4)HexNAc(3)Kdn(1) (S)</option>
@@ -3830,6 +4216,12 @@
       <option value="Diethylphosphate (S)">Diethylphosphate (S)</option>
       <option value="Diethylphosphate (T)">Diethylphosphate (T)</option>
       <option value="Diethylphosphate (Y)">Diethylphosphate (Y)</option>
+      <option value="Diethylphosphothione (C)">Diethylphosphothione (C)</option>
+      <option value="Diethylphosphothione (H)">Diethylphosphothione (H)</option>
+      <option value="Diethylphosphothione (K)">Diethylphosphothione (K)</option>
+      <option value="Diethylphosphothione (S)">Diethylphosphothione (S)</option>
+      <option value="Diethylphosphothione (T)">Diethylphosphothione (T)</option>
+      <option value="Diethylphosphothione (Y)">Diethylphosphothione (Y)</option>
       <option value="Difuran (Y)">Difuran (Y)</option>
       <option value="Dihydroxyimidazolidine (R)">Dihydroxyimidazolidine (R)</option>
       <option value="Diiodo (H)">Diiodo (H)</option>
@@ -3879,15 +4271,26 @@
       <option value="Dimethyl:2H(6)13C(2) (Protein N-term)">Dimethyl:2H(6)13C(2) (Protein N-term)</option>
       <option value="Dimethyl:2H(6)13C(2) (R)">Dimethyl:2H(6)13C(2) (R)</option>
       <option value="DimethylamineGMBS (C)">DimethylamineGMBS (C)</option>
+      <option value="Dimethylaminoethyl (C)">Dimethylaminoethyl (C)</option>
       <option value="DimethylArsino (C)">DimethylArsino (C)</option>
+      <option value="Dimethylphosphothione (C)">Dimethylphosphothione (C)</option>
+      <option value="Dimethylphosphothione (H)">Dimethylphosphothione (H)</option>
+      <option value="Dimethylphosphothione (K)">Dimethylphosphothione (K)</option>
+      <option value="Dimethylphosphothione (S)">Dimethylphosphothione (S)</option>
+      <option value="Dimethylphosphothione (T)">Dimethylphosphothione (T)</option>
+      <option value="Dimethylphosphothione (Y)">Dimethylphosphothione (Y)</option>
       <option value="DimethylpyrroleAdduct (K)">DimethylpyrroleAdduct (K)</option>
       <option value="Dioxidation (C)">Dioxidation (C)</option>
+      <option value="Dioxidation (E)">Dioxidation (E)</option>
       <option value="Dioxidation (F)">Dioxidation (F)</option>
+      <option value="Dioxidation (I)">Dioxidation (I)</option>
       <option value="Dioxidation (K)">Dioxidation (K)</option>
+      <option value="Dioxidation (L)">Dioxidation (L)</option>
       <option value="Dioxidation (M)">Dioxidation (M)</option>
       <option value="Dioxidation (P)">Dioxidation (P)</option>
       <option value="Dioxidation (R)">Dioxidation (R)</option>
       <option value="Dioxidation (U)">Dioxidation (U)</option>
+      <option value="Dioxidation (V)">Dioxidation (V)</option>
       <option value="Dioxidation (W)">Dioxidation (W)</option>
       <option value="Dioxidation (Y)">Dioxidation (Y)</option>
       <option value="Diphthamide (H)">Diphthamide (H)</option>
@@ -3904,18 +4307,9 @@
       <option value="dNIC (N-term)">dNIC (N-term)</option>
       <option value="DNPS (C)">DNPS (C)</option>
       <option value="DNPS (W)">DNPS (W)</option>
-      <option value="DTBP (K)">DTBP (K)</option>
-      <option value="DTBP (N)">DTBP (N)</option>
-      <option value="DTBP (Protein N-term)">DTBP (Protein N-term)</option>
-      <option value="DTBP (Q)">DTBP (Q)</option>
-      <option value="DTBP (R)">DTBP (R)</option>
-      <option value="DTT_C (C)">DTT_C (C)</option>
-      <option value="DTT_C:2H(6) (C)">DTT_C:2H(6) (C)</option>
-      <option value="DTT_ST (S)">DTT_ST (S)</option>
-      <option value="DTT_ST (T)">DTT_ST (T)</option>
-      <option value="DTT_ST:2H(6) (S)">DTT_ST:2H(6) (S)</option>
-      <option value="DTT_ST:2H(6) (T)">DTT_ST:2H(6) (T)</option>
+      <option value="DTT (C)">DTT (C)</option>
       <option value="DyLight-maleimide (C)">DyLight-maleimide (C)</option>
+      <option value="DYn-2 (C)">DYn-2 (C)</option>
       <option value="EDEDTIDVFQQQTGG (K)">EDEDTIDVFQQQTGG (K)</option>
       <option value="EDT-iodoacetyl-PEO-biotin (S)">EDT-iodoacetyl-PEO-biotin (S)</option>
       <option value="EDT-iodoacetyl-PEO-biotin (T)">EDT-iodoacetyl-PEO-biotin (T)</option>
@@ -3984,6 +4378,7 @@
       <option value="Formyl (Protein N-term)">Formyl (Protein N-term)</option>
       <option value="Formyl (S)">Formyl (S)</option>
       <option value="Formyl (T)">Formyl (T)</option>
+      <option value="Formylasparagine (H)">Formylasparagine (H)</option>
       <option value="FormylMet (Protein N-term)">FormylMet (Protein N-term)</option>
       <option value="FP-Biotin (K)">FP-Biotin (K)</option>
       <option value="FP-Biotin (S)">FP-Biotin (S)</option>
@@ -4002,6 +4397,7 @@
       <option value="GeranylGeranyl (C)">GeranylGeranyl (C)</option>
       <option value="GG (C)">GG (C)</option>
       <option value="GG (K)">GG (K)</option>
+      <option value="GG (Protein N-term)">GG (Protein N-term)</option>
       <option value="GG (S)">GG (S)</option>
       <option value="GG (T)">GG (T)</option>
       <option value="GGQ (K)">GGQ (K)</option>
@@ -4068,6 +4464,7 @@
       <option value="GluGluGlu (Protein C-term)">GluGluGlu (Protein C-term)</option>
       <option value="GluGluGluGlu (E)">GluGluGluGlu (E)</option>
       <option value="GluGluGluGlu (Protein C-term)">GluGluGluGlu (Protein C-term)</option>
+      <option value="Gluratylation (K)">Gluratylation (K)</option>
       <option value="Glutathione (C)">Glutathione (C)</option>
       <option value="Gly (K)">Gly (K)</option>
       <option value="Gly (S)">Gly (S)</option>
@@ -4096,9 +4493,17 @@
       <option value="glycidamide (K)">glycidamide (K)</option>
       <option value="glycidamide (N-term)">glycidamide (N-term)</option>
       <option value="Glycosyl (P)">Glycosyl (P)</option>
+      <option value="glyoxalAGE (R)">glyoxalAGE (R)</option>
+      <option value="GNLLFLACYCIGG (K)">GNLLFLACYCIGG (K)</option>
       <option value="GPIanchor (Protein C-term)">GPIanchor (Protein C-term)</option>
       <option value="Guanidinyl (K)">Guanidinyl (K)</option>
       <option value="Guanidinyl (N-term)">Guanidinyl (N-term)</option>
+      <option value="Haloxon (C)">Haloxon (C)</option>
+      <option value="Haloxon (H)">Haloxon (H)</option>
+      <option value="Haloxon (K)">Haloxon (K)</option>
+      <option value="Haloxon (S)">Haloxon (S)</option>
+      <option value="Haloxon (T)">Haloxon (T)</option>
+      <option value="Haloxon (Y)">Haloxon (Y)</option>
       <option value="HCysteinyl (C)">HCysteinyl (C)</option>
       <option value="HCysThiolactone (K)">HCysThiolactone (K)</option>
       <option value="Heme (C)">Heme (C)</option>
@@ -4178,6 +4583,8 @@
       <option value="Hex(1)HexNAc(2)dHex(2) (N)">Hex(1)HexNAc(2)dHex(2) (N)</option>
       <option value="Hex(1)HexNAc(2)dHex(2) (S)">Hex(1)HexNAc(2)dHex(2) (S)</option>
       <option value="Hex(1)HexNAc(2)dHex(2) (T)">Hex(1)HexNAc(2)dHex(2) (T)</option>
+      <option value="Hex(1)HexNAc(2)dHex(2)Sulf(1) (S)">Hex(1)HexNAc(2)dHex(2)Sulf(1) (S)</option>
+      <option value="Hex(1)HexNAc(2)dHex(2)Sulf(1) (T)">Hex(1)HexNAc(2)dHex(2)Sulf(1) (T)</option>
       <option value="Hex(1)HexNAc(2)NeuAc(1) (S)">Hex(1)HexNAc(2)NeuAc(1) (S)</option>
       <option value="Hex(1)HexNAc(2)NeuAc(1) (T)">Hex(1)HexNAc(2)NeuAc(1) (T)</option>
       <option value="Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)">Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
@@ -4201,6 +4608,8 @@
       <option value="Hex(1)HexNAc(3)NeuGc(1) (T)">Hex(1)HexNAc(3)NeuGc(1) (T)</option>
       <option value="Hex(1)HexNAc(3)Sulf(1) (S)">Hex(1)HexNAc(3)Sulf(1) (S)</option>
       <option value="Hex(1)HexNAc(3)Sulf(1) (T)">Hex(1)HexNAc(3)Sulf(1) (T)</option>
+      <option value="Hex(1)HexNAc(4)dHex(1)Sulf(1) (S)">Hex(1)HexNAc(4)dHex(1)Sulf(1) (S)</option>
+      <option value="Hex(1)HexNAc(4)dHex(1)Sulf(1) (T)">Hex(1)HexNAc(4)dHex(1)Sulf(1) (T)</option>
       <option value="Hex(1)NeuAc(1) (S)">Hex(1)NeuAc(1) (S)</option>
       <option value="Hex(1)NeuAc(1) (T)">Hex(1)NeuAc(1) (T)</option>
       <option value="Hex(1)NeuAc(1)Pent(1) (S)">Hex(1)NeuAc(1)Pent(1) (S)</option>
@@ -4211,16 +4620,26 @@
       <option value="Hex(1)Pent(1) (T)">Hex(1)Pent(1) (T)</option>
       <option value="Hex(1)Pent(2) (S)">Hex(1)Pent(2) (S)</option>
       <option value="Hex(1)Pent(2) (T)">Hex(1)Pent(2) (T)</option>
+      <option value="Hex(1)Pent(2)Me(1) (S)">Hex(1)Pent(2)Me(1) (S)</option>
+      <option value="Hex(1)Pent(2)Me(1) (T)">Hex(1)Pent(2)Me(1) (T)</option>
+      <option value="Hex(1)Pent(3) (S)">Hex(1)Pent(3) (S)</option>
+      <option value="Hex(1)Pent(3) (T)">Hex(1)Pent(3) (T)</option>
+      <option value="Hex(1)Pent(3)Me(1) (S)">Hex(1)Pent(3)Me(1) (S)</option>
+      <option value="Hex(1)Pent(3)Me(1) (T)">Hex(1)Pent(3)Me(1) (T)</option>
+      <option value="Hex(10)HexNAc(1) (N)">Hex(10)HexNAc(1) (N)</option>
       <option value="Hex(10)Phos(3) (S)">Hex(10)Phos(3) (S)</option>
       <option value="Hex(10)Phos(3) (T)">Hex(10)Phos(3) (T)</option>
       <option value="Hex(2) (K)">Hex(2) (K)</option>
       <option value="Hex(2) (R)">Hex(2) (R)</option>
+      <option value="Hex(2) (S)">Hex(2) (S)</option>
+      <option value="Hex(2) (T)">Hex(2) (T)</option>
       <option value="Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)">Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)</option>
       <option value="Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)">Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)</option>
       <option value="Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S)">Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S)</option>
       <option value="Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T)">Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T)</option>
       <option value="Hex(2)HexA(1)Pent(1)Sulf(1) (S)">Hex(2)HexA(1)Pent(1)Sulf(1) (S)</option>
       <option value="Hex(2)HexA(1)Pent(1)Sulf(1) (T)">Hex(2)HexA(1)Pent(1)Sulf(1) (T)</option>
+      <option value="Hex(2)HexNAc(1) (N)">Hex(2)HexNAc(1) (N)</option>
       <option value="Hex(2)HexNAc(1) (S)">Hex(2)HexNAc(1) (S)</option>
       <option value="Hex(2)HexNAc(1) (T)">Hex(2)HexNAc(1) (T)</option>
       <option value="Hex(2)HexNAc(1)Me(1) (S)">Hex(2)HexNAc(1)Me(1) (S)</option>
@@ -4233,6 +4652,8 @@
       <option value="Hex(2)HexNAc(1)NeuGc(3) (T)">Hex(2)HexNAc(1)NeuGc(3) (T)</option>
       <option value="Hex(2)HexNAc(1)NeuGc(4) (S)">Hex(2)HexNAc(1)NeuGc(4) (S)</option>
       <option value="Hex(2)HexNAc(1)NeuGc(4) (T)">Hex(2)HexNAc(1)NeuGc(4) (T)</option>
+      <option value="Hex(2)HexNAc(1)Pent(1)HexA(1) (S)">Hex(2)HexNAc(1)Pent(1)HexA(1) (S)</option>
+      <option value="Hex(2)HexNAc(1)Pent(1)HexA(1) (T)">Hex(2)HexNAc(1)Pent(1)HexA(1) (T)</option>
       <option value="Hex(2)HexNAc(1)Sulf(1) (S)">Hex(2)HexNAc(1)Sulf(1) (S)</option>
       <option value="Hex(2)HexNAc(1)Sulf(1) (T)">Hex(2)HexNAc(1)Sulf(1) (T)</option>
       <option value="Hex(2)HexNAc(2) (N)">Hex(2)HexNAc(2) (N)</option>
@@ -4242,6 +4663,8 @@
       <option value="Hex(2)HexNAc(2)dHex(1) (S)">Hex(2)HexNAc(2)dHex(1) (S)</option>
       <option value="Hex(2)HexNAc(2)dHex(1) (T)">Hex(2)HexNAc(2)dHex(1) (T)</option>
       <option value="Hex(2)HexNAc(2)NeuAc(1) (N)">Hex(2)HexNAc(2)NeuAc(1) (N)</option>
+      <option value="Hex(2)HexNAc(2)NeuAc(1) (S)">Hex(2)HexNAc(2)NeuAc(1) (S)</option>
+      <option value="Hex(2)HexNAc(2)NeuAc(1) (T)">Hex(2)HexNAc(2)NeuAc(1) (T)</option>
       <option value="Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
       <option value="Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
       <option value="Hex(2)HexNAc(2)NeuAc(2) (S)">Hex(2)HexNAc(2)NeuAc(2) (S)</option>
@@ -4253,6 +4676,7 @@
       <option value="Hex(2)HexNAc(2)Pent(1) (N)">Hex(2)HexNAc(2)Pent(1) (N)</option>
       <option value="Hex(2)HexNAc(2)Sulf(1) (S)">Hex(2)HexNAc(2)Sulf(1) (S)</option>
       <option value="Hex(2)HexNAc(2)Sulf(1) (T)">Hex(2)HexNAc(2)Sulf(1) (T)</option>
+      <option value="Hex(2)HexNAc(3) (N)">Hex(2)HexNAc(3) (N)</option>
       <option value="Hex(2)HexNAc(3) (S)">Hex(2)HexNAc(3) (S)</option>
       <option value="Hex(2)HexNAc(3) (T)">Hex(2)HexNAc(3) (T)</option>
       <option value="Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S)">Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S)</option>
@@ -4271,6 +4695,7 @@
       <option value="Hex(2)HexNAc(3)NeuGc(3) (T)">Hex(2)HexNAc(3)NeuGc(3) (T)</option>
       <option value="Hex(2)HexNAc(3)Sulf(1) (S)">Hex(2)HexNAc(3)Sulf(1) (S)</option>
       <option value="Hex(2)HexNAc(3)Sulf(1) (T)">Hex(2)HexNAc(3)Sulf(1) (T)</option>
+      <option value="Hex(2)HexNAc(4) (N)">Hex(2)HexNAc(4) (N)</option>
       <option value="Hex(2)HexNAc(4) (S)">Hex(2)HexNAc(4) (S)</option>
       <option value="Hex(2)HexNAc(4) (T)">Hex(2)HexNAc(4) (T)</option>
       <option value="Hex(2)HexNAc(4)NeuAc(1) (S)">Hex(2)HexNAc(4)NeuAc(1) (S)</option>
@@ -4279,11 +4704,20 @@
       <option value="Hex(2)HexNAc(5) (T)">Hex(2)HexNAc(5) (T)</option>
       <option value="Hex(2)NeuAc(1) (S)">Hex(2)NeuAc(1) (S)</option>
       <option value="Hex(2)NeuAc(1) (T)">Hex(2)NeuAc(1) (T)</option>
+      <option value="Hex(2)Pent(2) (S)">Hex(2)Pent(2) (S)</option>
+      <option value="Hex(2)Pent(2) (T)">Hex(2)Pent(2) (T)</option>
+      <option value="Hex(2)Pent(2)Me(1) (S)">Hex(2)Pent(2)Me(1) (S)</option>
+      <option value="Hex(2)Pent(2)Me(1) (T)">Hex(2)Pent(2)Me(1) (T)</option>
+      <option value="Hex(2)Sulf(1) (S)">Hex(2)Sulf(1) (S)</option>
+      <option value="Hex(2)Sulf(1) (T)">Hex(2)Sulf(1) (T)</option>
       <option value="Hex(3) (N)">Hex(3) (N)</option>
       <option value="Hex(3) (S)">Hex(3) (S)</option>
       <option value="Hex(3) (T)">Hex(3) (T)</option>
+      <option value="Hex(3)HexNAc(1) (N)">Hex(3)HexNAc(1) (N)</option>
       <option value="Hex(3)HexNAc(1) (S)">Hex(3)HexNAc(1) (S)</option>
       <option value="Hex(3)HexNAc(1) (T)">Hex(3)HexNAc(1) (T)</option>
+      <option value="Hex(3)HexNAc(1)HexA(1) (S)">Hex(3)HexNAc(1)HexA(1) (S)</option>
+      <option value="Hex(3)HexNAc(1)HexA(1) (T)">Hex(3)HexNAc(1)HexA(1) (T)</option>
       <option value="Hex(3)HexNAc(1)Me(1) (S)">Hex(3)HexNAc(1)Me(1) (S)</option>
       <option value="Hex(3)HexNAc(1)Me(1) (T)">Hex(3)HexNAc(1)Me(1) (T)</option>
       <option value="Hex(3)HexNAc(1)Pent(1) (N)">Hex(3)HexNAc(1)Pent(1) (N)</option>
@@ -4306,22 +4740,27 @@
       <option value="Hex(3)HexNAc(3)NeuAc(2) (T)">Hex(3)HexNAc(3)NeuAc(2) (T)</option>
       <option value="Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S)">Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S)</option>
       <option value="Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T)">Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T)</option>
+      <option value="Hex(3)HexNAc(3)NeuAc(3) (S)">Hex(3)HexNAc(3)NeuAc(3) (S)</option>
+      <option value="Hex(3)HexNAc(3)NeuAc(3) (T)">Hex(3)HexNAc(3)NeuAc(3) (T)</option>
       <option value="Hex(3)HexNAc(3)NeuGc(1) (S)">Hex(3)HexNAc(3)NeuGc(1) (S)</option>
       <option value="Hex(3)HexNAc(3)NeuGc(1) (T)">Hex(3)HexNAc(3)NeuGc(1) (T)</option>
       <option value="Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S)">Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S)</option>
       <option value="Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T)">Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T)</option>
       <option value="Hex(3)HexNAc(3)Pent(1) (N)">Hex(3)HexNAc(3)Pent(1) (N)</option>
+      <option value="Hex(3)HexNAc(3)Sulf(1) (N)">Hex(3)HexNAc(3)Sulf(1) (N)</option>
       <option value="Hex(3)HexNAc(3)Sulf(1) (S)">Hex(3)HexNAc(3)Sulf(1) (S)</option>
       <option value="Hex(3)HexNAc(3)Sulf(1) (T)">Hex(3)HexNAc(3)Sulf(1) (T)</option>
       <option value="Hex(3)HexNAc(4) (N)">Hex(3)HexNAc(4) (N)</option>
       <option value="Hex(3)HexNAc(4) (S)">Hex(3)HexNAc(4) (S)</option>
       <option value="Hex(3)HexNAc(4) (T)">Hex(3)HexNAc(4) (T)</option>
       <option value="Hex(3)HexNAc(4)NeuAc(1) (N)">Hex(3)HexNAc(4)NeuAc(1) (N)</option>
+      <option value="Hex(3)HexNAc(4)NeuAc(2) (N)">Hex(3)HexNAc(4)NeuAc(2) (N)</option>
       <option value="Hex(3)HexNAc(4)Pent(1) (N)">Hex(3)HexNAc(4)Pent(1) (N)</option>
       <option value="Hex(3)HexNAc(4)Sulf(1) (N)">Hex(3)HexNAc(4)Sulf(1) (N)</option>
       <option value="Hex(3)HexNAc(5) (N)">Hex(3)HexNAc(5) (N)</option>
       <option value="Hex(3)HexNAc(5) (S)">Hex(3)HexNAc(5) (S)</option>
       <option value="Hex(3)HexNAc(5) (T)">Hex(3)HexNAc(5) (T)</option>
+      <option value="Hex(3)HexNAc(5)NeuAc(1) (N)">Hex(3)HexNAc(5)NeuAc(1) (N)</option>
       <option value="Hex(3)HexNAc(5)Sulf(1) (N)">Hex(3)HexNAc(5)Sulf(1) (N)</option>
       <option value="Hex(3)HexNAc(6) (N)">Hex(3)HexNAc(6) (N)</option>
       <option value="Hex(3)HexNAc(6) (S)">Hex(3)HexNAc(6) (S)</option>
@@ -4331,14 +4770,19 @@
       <option value="Hex(3)HexNAc(6)Sulf(2) (N)">Hex(3)HexNAc(6)Sulf(2) (N)</option>
       <option value="Hex(3)HexNAc(7) (N)">Hex(3)HexNAc(7) (N)</option>
       <option value="Hex(3)HexNAc(7)Sulf(1) (N)">Hex(3)HexNAc(7)Sulf(1) (N)</option>
-      <option value="Hex(3)Phos(1) (S)">Hex(3)Phos(1) (S)</option>
-      <option value="Hex(3)Phos(1) (T)">Hex(3)Phos(1) (T)</option>
       <option value="Hex(4) (S)">Hex(4) (S)</option>
       <option value="Hex(4) (T)">Hex(4) (T)</option>
+      <option value="Hex(4)HexA(1) (S)">Hex(4)HexA(1) (S)</option>
+      <option value="Hex(4)HexA(1) (T)">Hex(4)HexA(1) (T)</option>
+      <option value="Hex(4)HexA(1)HexNAc(1) (S)">Hex(4)HexA(1)HexNAc(1) (S)</option>
+      <option value="Hex(4)HexA(1)HexNAc(1) (T)">Hex(4)HexA(1)HexNAc(1) (T)</option>
+      <option value="Hex(4)HexNAc(1) (N)">Hex(4)HexNAc(1) (N)</option>
       <option value="Hex(4)HexNAc(1) (S)">Hex(4)HexNAc(1) (S)</option>
       <option value="Hex(4)HexNAc(1) (T)">Hex(4)HexNAc(1) (T)</option>
       <option value="Hex(4)HexNAc(2) (N)">Hex(4)HexNAc(2) (N)</option>
       <option value="Hex(4)HexNAc(2)NeuAc(1) (N)">Hex(4)HexNAc(2)NeuAc(1) (N)</option>
+      <option value="Hex(4)HexNAc(2)NeuAc(1) (S)">Hex(4)HexNAc(2)NeuAc(1) (S)</option>
+      <option value="Hex(4)HexNAc(2)NeuAc(1) (T)">Hex(4)HexNAc(2)NeuAc(1) (T)</option>
       <option value="Hex(4)HexNAc(2)Pent(1) (N)">Hex(4)HexNAc(2)Pent(1) (N)</option>
       <option value="Hex(4)HexNAc(3) (N)">Hex(4)HexNAc(3) (N)</option>
       <option value="Hex(4)HexNAc(3) (S)">Hex(4)HexNAc(3) (S)</option>
@@ -4360,6 +4804,9 @@
       <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T)">Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T)</option>
       <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S)">Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S)</option>
       <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T)">Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T)</option>
+      <option value="Hex(4)HexNAc(4)NeuGc(1) (N)">Hex(4)HexNAc(4)NeuGc(1) (N)</option>
+      <option value="Hex(4)HexNAc(4)NeuGc(1) (S)">Hex(4)HexNAc(4)NeuGc(1) (S)</option>
+      <option value="Hex(4)HexNAc(4)NeuGc(1) (T)">Hex(4)HexNAc(4)NeuGc(1) (T)</option>
       <option value="Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S)">Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S)</option>
       <option value="Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T)">Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T)</option>
       <option value="Hex(4)HexNAc(4)Pent(1) (N)">Hex(4)HexNAc(4)Pent(1) (N)</option>
@@ -4374,6 +4821,9 @@
       <option value="Hex(4)Phos(1) (T)">Hex(4)Phos(1) (T)</option>
       <option value="Hex(5) (S)">Hex(5) (S)</option>
       <option value="Hex(5) (T)">Hex(5) (T)</option>
+      <option value="Hex(5)HexA(1) (S)">Hex(5)HexA(1) (S)</option>
+      <option value="Hex(5)HexA(1) (T)">Hex(5)HexA(1) (T)</option>
+      <option value="Hex(5)HexNAc(1) (N)">Hex(5)HexNAc(1) (N)</option>
       <option value="Hex(5)HexNAc(1) (S)">Hex(5)HexNAc(1) (S)</option>
       <option value="Hex(5)HexNAc(1) (T)">Hex(5)HexNAc(1) (T)</option>
       <option value="Hex(5)HexNAc(2) (N)">Hex(5)HexNAc(2) (N)</option>
@@ -4385,6 +4835,8 @@
       <option value="Hex(5)HexNAc(4) (T)">Hex(5)HexNAc(4) (T)</option>
       <option value="Hex(5)HexNAc(4)Me(2)Pent(1) (N)">Hex(5)HexNAc(4)Me(2)Pent(1) (N)</option>
       <option value="Hex(5)HexNAc(4)NeuAc(1) (N)">Hex(5)HexNAc(4)NeuAc(1) (N)</option>
+      <option value="Hex(5)HexNAc(4)NeuAc(1)Ac(1) (N)">Hex(5)HexNAc(4)NeuAc(1)Ac(1) (N)</option>
+      <option value="Hex(5)HexNAc(4)NeuAc(1)Ac(2) (N)">Hex(5)HexNAc(4)NeuAc(1)Ac(2) (N)</option>
       <option value="Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N)">Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N)</option>
       <option value="Hex(5)HexNAc(4)NeuAc(2) (N)">Hex(5)HexNAc(4)NeuAc(2) (N)</option>
       <option value="Hex(5)HexNAc(4)NeuGc(1) (N)">Hex(5)HexNAc(4)NeuGc(1) (N)</option>
@@ -4396,6 +4848,7 @@
       <option value="Hex(5)Phos(1) (T)">Hex(5)Phos(1) (T)</option>
       <option value="Hex(5)Phos(3) (S)">Hex(5)Phos(3) (S)</option>
       <option value="Hex(5)Phos(3) (T)">Hex(5)Phos(3) (T)</option>
+      <option value="Hex(6)HexNAc(1) (N)">Hex(6)HexNAc(1) (N)</option>
       <option value="Hex(6)HexNAc(2) (N)">Hex(6)HexNAc(2) (N)</option>
       <option value="Hex(6)HexNAc(2)Phos(1) (N)">Hex(6)HexNAc(2)Phos(1) (N)</option>
       <option value="Hex(6)HexNAc(3) (N)">Hex(6)HexNAc(3) (N)</option>
@@ -4423,14 +4876,19 @@
       <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option>
       <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option>
       <option value="Hex(8)Phos(3) (T)">Hex(8)Phos(3) (T)</option>
+      <option value="Hex(9) (N)">Hex(9) (N)</option>
+      <option value="Hex(9)HexNAc(1) (N)">Hex(9)HexNAc(1) (N)</option>
       <option value="Hex(9)HexNAc(2) (N)">Hex(9)HexNAc(2) (N)</option>
       <option value="Hex(9)Phos(3) (S)">Hex(9)Phos(3) (S)</option>
       <option value="Hex(9)Phos(3) (T)">Hex(9)Phos(3) (T)</option>
+      <option value="HexA(2)HexNAc(3) (S)">HexA(2)HexNAc(3) (S)</option>
+      <option value="HexA(2)HexNAc(3) (T)">HexA(2)HexNAc(3) (T)</option>
       <option value="HexN (K)">HexN (K)</option>
       <option value="HexN (N)">HexN (N)</option>
       <option value="HexN (S)">HexN (S)</option>
       <option value="HexN (T)">HexN (T)</option>
       <option value="HexN (W)">HexN (W)</option>
+      <option value="HexNAc (C)">HexNAc (C)</option>
       <option value="HexNAc (N)">HexNAc (N)</option>
       <option value="HexNAc (S)">HexNAc (S)</option>
       <option value="HexNAc (T)">HexNAc (T)</option>
@@ -4457,6 +4915,8 @@
       <option value="HexNAc(2)NeuAc(1)Sulf(1) (T)">HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
       <option value="HexNAc(2)NeuGc(1) (S)">HexNAc(2)NeuGc(1) (S)</option>
       <option value="HexNAc(2)NeuGc(1) (T)">HexNAc(2)NeuGc(1) (T)</option>
+      <option value="HexNAc(2)Sulf(1) (S)">HexNAc(2)Sulf(1) (S)</option>
+      <option value="HexNAc(2)Sulf(1) (T)">HexNAc(2)Sulf(1) (T)</option>
       <option value="HexNAc(3) (S)">HexNAc(3) (S)</option>
       <option value="HexNAc(3) (T)">HexNAc(3) (T)</option>
       <option value="HexNAc(3)Sulf(1) (S)">HexNAc(3)Sulf(1) (S)</option>
@@ -4511,6 +4971,7 @@
       <option value="Hydroxycinnamyl (C)">Hydroxycinnamyl (C)</option>
       <option value="Hydroxyfarnesyl (C)">Hydroxyfarnesyl (C)</option>
       <option value="Hydroxyheme (E)">Hydroxyheme (E)</option>
+      <option value="hydroxyisobutyryl (K)">hydroxyisobutyryl (K)</option>
       <option value="Hydroxymethyl (N)">Hydroxymethyl (N)</option>
       <option value="HydroxymethylOP (K)">HydroxymethylOP (K)</option>
       <option value="Hydroxytrimethyl (K)">Hydroxytrimethyl (K)</option>
@@ -4573,6 +5034,7 @@
       <option value="Isopropylphospho (S)">Isopropylphospho (S)</option>
       <option value="Isopropylphospho (T)">Isopropylphospho (T)</option>
       <option value="Isopropylphospho (Y)">Isopropylphospho (Y)</option>
+      <option value="iTRAQ4plex (C)">iTRAQ4plex (C)</option>
       <option value="iTRAQ4plex (H)">iTRAQ4plex (H)</option>
       <option value="iTRAQ4plex (K)">iTRAQ4plex (K)</option>
       <option value="iTRAQ4plex (N-term)">iTRAQ4plex (N-term)</option>
@@ -4580,12 +5042,15 @@
       <option value="iTRAQ4plex (S)">iTRAQ4plex (S)</option>
       <option value="iTRAQ4plex (T)">iTRAQ4plex (T)</option>
       <option value="iTRAQ4plex (Y)">iTRAQ4plex (Y)</option>
+      <option value="iTRAQ4plex114 (C)">iTRAQ4plex114 (C)</option>
       <option value="iTRAQ4plex114 (K)">iTRAQ4plex114 (K)</option>
       <option value="iTRAQ4plex114 (N-term)">iTRAQ4plex114 (N-term)</option>
       <option value="iTRAQ4plex114 (Y)">iTRAQ4plex114 (Y)</option>
+      <option value="iTRAQ4plex115 (C)">iTRAQ4plex115 (C)</option>
       <option value="iTRAQ4plex115 (K)">iTRAQ4plex115 (K)</option>
       <option value="iTRAQ4plex115 (N-term)">iTRAQ4plex115 (N-term)</option>
       <option value="iTRAQ4plex115 (Y)">iTRAQ4plex115 (Y)</option>
+      <option value="iTRAQ8plex (C)">iTRAQ8plex (C)</option>
       <option value="iTRAQ8plex (H)">iTRAQ8plex (H)</option>
       <option value="iTRAQ8plex (K)">iTRAQ8plex (K)</option>
       <option value="iTRAQ8plex (N-term)">iTRAQ8plex (N-term)</option>
@@ -4593,6 +5058,7 @@
       <option value="iTRAQ8plex (S)">iTRAQ8plex (S)</option>
       <option value="iTRAQ8plex (T)">iTRAQ8plex (T)</option>
       <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option>
+      <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
@@ -4662,8 +5128,10 @@
       <option value="Label:2H(3) (L)">Label:2H(3) (L)</option>
       <option value="Label:2H(3) (M)">Label:2H(3) (M)</option>
       <option value="Label:2H(3)+Oxidation (M)">Label:2H(3)+Oxidation (M)</option>
+      <option value="Label:2H(4) (A)">Label:2H(4) (A)</option>
       <option value="Label:2H(4) (F)">Label:2H(4) (F)</option>
       <option value="Label:2H(4) (K)">Label:2H(4) (K)</option>
+      <option value="Label:2H(4) (U)">Label:2H(4) (U)</option>
       <option value="Label:2H(4) (Y)">Label:2H(4) (Y)</option>
       <option value="Label:2H(4)+Acetyl (K)">Label:2H(4)+Acetyl (K)</option>
       <option value="Label:2H(4)+GG (K)">Label:2H(4)+GG (K)</option>
@@ -4722,19 +5190,25 @@
       <option value="maleimide5 (C)">maleimide5 (C)</option>
       <option value="maleimide5 (K)">maleimide5 (K)</option>
       <option value="Malonyl (C)">Malonyl (C)</option>
+      <option value="Malonyl (K)">Malonyl (K)</option>
       <option value="Malonyl (S)">Malonyl (S)</option>
       <option value="MDCC (C)">MDCC (C)</option>
+      <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
       <option value="Menadione (C)">Menadione (C)</option>
       <option value="Menadione (K)">Menadione (K)</option>
       <option value="Menadione-HQ (C)">Menadione-HQ (C)</option>
       <option value="Menadione-HQ (K)">Menadione-HQ (K)</option>
       <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option>
       <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option>
+      <option value="MesitylOxide (H)">MesitylOxide (H)</option>
+      <option value="MesitylOxide (K)">MesitylOxide (K)</option>
+      <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
       <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
       <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
       <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
       <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option>
       <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option>
+      <option value="Met-&gt;AspSA (M)">Met-&gt;AspSA (M)</option>
       <option value="Met-&gt;Cys (M)">Met-&gt;Cys (M)</option>
       <option value="Met-&gt;Gln (M)">Met-&gt;Gln (M)</option>
       <option value="Met-&gt;Glu (M)">Met-&gt;Glu (M)</option>
@@ -4754,6 +5228,18 @@
       <option value="Met-&gt;Xle (M)">Met-&gt;Xle (M)</option>
       <option value="Met-loss (Protein N-term M)">Met-loss (Protein N-term M)</option>
       <option value="Met-loss+Acetyl (Protein N-term M)">Met-loss+Acetyl (Protein N-term M)</option>
+      <option value="Methamidophos-O (C)">Methamidophos-O (C)</option>
+      <option value="Methamidophos-O (H)">Methamidophos-O (H)</option>
+      <option value="Methamidophos-O (K)">Methamidophos-O (K)</option>
+      <option value="Methamidophos-O (S)">Methamidophos-O (S)</option>
+      <option value="Methamidophos-O (T)">Methamidophos-O (T)</option>
+      <option value="Methamidophos-O (Y)">Methamidophos-O (Y)</option>
+      <option value="Methamidophos-S (C)">Methamidophos-S (C)</option>
+      <option value="Methamidophos-S (H)">Methamidophos-S (H)</option>
+      <option value="Methamidophos-S (K)">Methamidophos-S (K)</option>
+      <option value="Methamidophos-S (S)">Methamidophos-S (S)</option>
+      <option value="Methamidophos-S (T)">Methamidophos-S (T)</option>
+      <option value="Methamidophos-S (Y)">Methamidophos-S (Y)</option>
       <option value="Methyl (C)">Methyl (C)</option>
       <option value="Methyl (C-term)">Methyl (C-term)</option>
       <option value="Methyl (D)">Methyl (D)</option>
@@ -4802,6 +5288,9 @@
       <option value="Methylamine (S)">Methylamine (S)</option>
       <option value="Methylamine (T)">Methylamine (T)</option>
       <option value="Methylmalonylation (S)">Methylmalonylation (S)</option>
+      <option value="methylol (K)">methylol (K)</option>
+      <option value="methylol (W)">methylol (W)</option>
+      <option value="methylol (Y)">methylol (Y)</option>
       <option value="Methylphosphonate (S)">Methylphosphonate (S)</option>
       <option value="Methylphosphonate (T)">Methylphosphonate (T)</option>
       <option value="Methylphosphonate (Y)">Methylphosphonate (Y)</option>
@@ -4823,6 +5312,12 @@
       <option value="MolybdopterinGD (D)">MolybdopterinGD (D)</option>
       <option value="MolybdopterinGD (U)">MolybdopterinGD (U)</option>
       <option value="MolybdopterinGD+Delta:S(-1)Se(1) (C)">MolybdopterinGD+Delta:S(-1)Se(1) (C)</option>
+      <option value="monomethylphosphothione (C)">monomethylphosphothione (C)</option>
+      <option value="monomethylphosphothione (H)">monomethylphosphothione (H)</option>
+      <option value="monomethylphosphothione (K)">monomethylphosphothione (K)</option>
+      <option value="monomethylphosphothione (S)">monomethylphosphothione (S)</option>
+      <option value="monomethylphosphothione (T)">monomethylphosphothione (T)</option>
+      <option value="monomethylphosphothione (Y)">monomethylphosphothione (Y)</option>
       <option value="mTRAQ (H)">mTRAQ (H)</option>
       <option value="mTRAQ (K)">mTRAQ (K)</option>
       <option value="mTRAQ (N-term)">mTRAQ (N-term)</option>
@@ -4880,9 +5375,12 @@
       <option value="NIC (K)">NIC (K)</option>
       <option value="NIC (N-term)">NIC (N-term)</option>
       <option value="NIPCAM (C)">NIPCAM (C)</option>
+      <option value="Nitrene (Y)">Nitrene (Y)</option>
+      <option value="Nitro (F)">Nitro (F)</option>
       <option value="Nitro (W)">Nitro (W)</option>
       <option value="Nitro (Y)">Nitro (Y)</option>
       <option value="Nitrosyl (C)">Nitrosyl (C)</option>
+      <option value="Nitrosyl (Y)">Nitrosyl (Y)</option>
       <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option>
       <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option>
       <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
@@ -4914,14 +5412,21 @@
       <option value="Oxidation (C)">Oxidation (C)</option>
       <option value="Oxidation (C-term G)">Oxidation (C-term G)</option>
       <option value="Oxidation (D)">Oxidation (D)</option>
+      <option value="Oxidation (E)">Oxidation (E)</option>
       <option value="Oxidation (F)">Oxidation (F)</option>
       <option value="Oxidation (H)">Oxidation (H)</option>
+      <option value="Oxidation (I)">Oxidation (I)</option>
       <option value="Oxidation (K)">Oxidation (K)</option>
+      <option value="Oxidation (L)">Oxidation (L)</option>
       <option value="Oxidation (M)" selected="true">Oxidation (M)</option>
       <option value="Oxidation (N)">Oxidation (N)</option>
       <option value="Oxidation (P)">Oxidation (P)</option>
+      <option value="Oxidation (Q)">Oxidation (Q)</option>
       <option value="Oxidation (R)">Oxidation (R)</option>
+      <option value="Oxidation (S)">Oxidation (S)</option>
+      <option value="Oxidation (T)">Oxidation (T)</option>
       <option value="Oxidation (U)">Oxidation (U)</option>
+      <option value="Oxidation (V)">Oxidation (V)</option>
       <option value="Oxidation (W)">Oxidation (W)</option>
       <option value="Oxidation (Y)">Oxidation (Y)</option>
       <option value="Oxidation+NEM (C)">Oxidation+NEM (C)</option>
@@ -4940,6 +5445,10 @@
       <option value="PEITC (C)">PEITC (C)</option>
       <option value="PEITC (K)">PEITC (K)</option>
       <option value="PEITC (N-term)">PEITC (N-term)</option>
+      <option value="Pent(1)HexNAc(1) (S)">Pent(1)HexNAc(1) (S)</option>
+      <option value="Pent(1)HexNAc(1) (T)">Pent(1)HexNAc(1) (T)</option>
+      <option value="Pent(2) (S)">Pent(2) (S)</option>
+      <option value="Pent(2) (T)">Pent(2) (T)</option>
       <option value="Pentose (S)">Pentose (S)</option>
       <option value="Pentose (T)">Pentose (T)</option>
       <option value="Pentylamine (Q)">Pentylamine (Q)</option>
@@ -4970,6 +5479,7 @@
       <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
       <option value="Phospho (C)">Phospho (C)</option>
       <option value="Phospho (D)">Phospho (D)</option>
+      <option value="Phospho (E)">Phospho (E)</option>
       <option value="Phospho (H)">Phospho (H)</option>
       <option value="Phospho (K)">Phospho (K)</option>
       <option value="Phospho (R)">Phospho (R)</option>
@@ -4980,6 +5490,9 @@
       <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
       <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
       <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
+      <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
+      <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option>
+      <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option>
       <option value="Phosphogluconoylation (K)">Phosphogluconoylation (K)</option>
       <option value="Phosphogluconoylation (N-term)">Phosphogluconoylation (N-term)</option>
       <option value="Phosphoguanosine (H)">Phosphoguanosine (H)</option>
@@ -5014,6 +5527,7 @@
       <option value="Pro-&gt;Gln (P)">Pro-&gt;Gln (P)</option>
       <option value="Pro-&gt;Glu (P)">Pro-&gt;Glu (P)</option>
       <option value="Pro-&gt;Gly (P)">Pro-&gt;Gly (P)</option>
+      <option value="Pro-&gt;HAVA (P)">Pro-&gt;HAVA (P)</option>
       <option value="Pro-&gt;His (P)">Pro-&gt;His (P)</option>
       <option value="Pro-&gt;Lys (P)">Pro-&gt;Lys (P)</option>
       <option value="Pro-&gt;Met (P)">Pro-&gt;Met (P)</option>
@@ -5117,9 +5631,12 @@
       <option value="Ser-&gt;Tyr (S)">Ser-&gt;Tyr (S)</option>
       <option value="Ser-&gt;Val (S)">Ser-&gt;Val (S)</option>
       <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option>
+      <option value="serotonylation (Q)">serotonylation (Q)</option>
+      <option value="shTMT (K)">shTMT (K)</option>
+      <option value="shTMT (N-term)">shTMT (N-term)</option>
+      <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
       <option value="SMA (K)">SMA (K)</option>
       <option value="SMA (N-term)">SMA (N-term)</option>
-      <option value="SMCC-maleimide (C)">SMCC-maleimide (C)</option>
       <option value="spermidine (Q)">spermidine (Q)</option>
       <option value="spermine (Q)">spermine (Q)</option>
       <option value="SPITC (K)">SPITC (K)</option>
@@ -5156,9 +5673,14 @@
       <option value="TAMRA-FP (S)">TAMRA-FP (S)</option>
       <option value="TAMRA-FP (Y)">TAMRA-FP (Y)</option>
       <option value="Thiadiazole (C)">Thiadiazole (C)</option>
-      <option value="Thiazolidine (N-term C)">Thiazolidine (N-term C)</option>
-      <option value="Thioacyl (K)">Thioacyl (K)</option>
-      <option value="Thioacyl (X)">Thioacyl (X)</option>
+      <option value="Thiazolidine (C)">Thiazolidine (C)</option>
+      <option value="Thiazolidine (F)">Thiazolidine (F)</option>
+      <option value="Thiazolidine (H)">Thiazolidine (H)</option>
+      <option value="Thiazolidine (K)">Thiazolidine (K)</option>
+      <option value="Thiazolidine (Protein N-term)">Thiazolidine (Protein N-term)</option>
+      <option value="Thiazolidine (R)">Thiazolidine (R)</option>
+      <option value="Thiazolidine (W)">Thiazolidine (W)</option>
+      <option value="Thiazolidine (Y)">Thiazolidine (Y)</option>
       <option value="thioacylPA (K)">thioacylPA (K)</option>
       <option value="Thiophos-S-S-biotin (S)">Thiophos-S-S-biotin (S)</option>
       <option value="Thiophos-S-S-biotin (T)">Thiophos-S-S-biotin (T)</option>
@@ -5190,7 +5712,12 @@
       <option value="TMAB (N-term)">TMAB (N-term)</option>
       <option value="TMAB:2H(9) (K)">TMAB:2H(9) (K)</option>
       <option value="TMAB:2H(9) (N-term)">TMAB:2H(9) (N-term)</option>
+      <option value="TMPP-Ac (K)">TMPP-Ac (K)</option>
       <option value="TMPP-Ac (N-term)">TMPP-Ac (N-term)</option>
+      <option value="TMPP-Ac (Y)">TMPP-Ac (Y)</option>
+      <option value="TMPP-Ac:13C(9) (K)">TMPP-Ac:13C(9) (K)</option>
+      <option value="TMPP-Ac:13C(9) (N-term)">TMPP-Ac:13C(9) (N-term)</option>
+      <option value="TMPP-Ac:13C(9) (Y)">TMPP-Ac:13C(9) (Y)</option>
       <option value="TMT (H)">TMT (H)</option>
       <option value="TMT (K)">TMT (K)</option>
       <option value="TMT (N-term)">TMT (N-term)</option>
@@ -5209,6 +5736,18 @@
       <option value="TMT6plex (Protein N-term)">TMT6plex (Protein N-term)</option>
       <option value="TMT6plex (S)">TMT6plex (S)</option>
       <option value="TMT6plex (T)">TMT6plex (T)</option>
+      <option value="TMTpro (H)">TMTpro (H)</option>
+      <option value="TMTpro (K)">TMTpro (K)</option>
+      <option value="TMTpro (N-term)">TMTpro (N-term)</option>
+      <option value="TMTpro (Protein N-term)">TMTpro (Protein N-term)</option>
+      <option value="TMTpro (S)">TMTpro (S)</option>
+      <option value="TMTpro (T)">TMTpro (T)</option>
+      <option value="TMTpro_zero (H)">TMTpro_zero (H)</option>
+      <option value="TMTpro_zero (K)">TMTpro_zero (K)</option>
+      <option value="TMTpro_zero (N-term)">TMTpro_zero (N-term)</option>
+      <option value="TMTpro_zero (Protein N-term)">TMTpro_zero (Protein N-term)</option>
+      <option value="TMTpro_zero (S)">TMTpro_zero (S)</option>
+      <option value="TMTpro_zero (T)">TMTpro_zero (T)</option>
       <option value="TNBS (K)">TNBS (K)</option>
       <option value="TNBS (N-term)">TNBS (N-term)</option>
       <option value="trifluoro (L)">trifluoro (L)</option>
@@ -5222,6 +5761,7 @@
       <option value="Trimethyl:2H(9) (K)">Trimethyl:2H(9) (K)</option>
       <option value="Trimethyl:2H(9) (R)">Trimethyl:2H(9) (R)</option>
       <option value="Trioxidation (C)">Trioxidation (C)</option>
+      <option value="Trioxidation (F)">Trioxidation (F)</option>
       <option value="Trioxidation (W)">Trioxidation (W)</option>
       <option value="Trioxidation (Y)">Trioxidation (Y)</option>
       <option value="Tripalmitate (Protein N-term C)">Tripalmitate (Protein N-term C)</option>
@@ -5280,6 +5820,44 @@
       <option value="UgiJoullieProGly (E)">UgiJoullieProGly (E)</option>
       <option value="UgiJoullieProGlyProGly (D)">UgiJoullieProGlyProGly (D)</option>
       <option value="UgiJoullieProGlyProGly (E)">UgiJoullieProGlyProGly (E)</option>
+      <option value="Unknown:162 (C-term)">Unknown:162 (C-term)</option>
+      <option value="Unknown:162 (D)">Unknown:162 (D)</option>
+      <option value="Unknown:162 (E)">Unknown:162 (E)</option>
+      <option value="Unknown:162 (N-term)">Unknown:162 (N-term)</option>
+      <option value="Unknown:177 (C-term)">Unknown:177 (C-term)</option>
+      <option value="Unknown:177 (D)">Unknown:177 (D)</option>
+      <option value="Unknown:177 (E)">Unknown:177 (E)</option>
+      <option value="Unknown:177 (N-term)">Unknown:177 (N-term)</option>
+      <option value="Unknown:210 (C-term)">Unknown:210 (C-term)</option>
+      <option value="Unknown:210 (D)">Unknown:210 (D)</option>
+      <option value="Unknown:210 (E)">Unknown:210 (E)</option>
+      <option value="Unknown:210 (N-term)">Unknown:210 (N-term)</option>
+      <option value="Unknown:216 (C-term)">Unknown:216 (C-term)</option>
+      <option value="Unknown:216 (D)">Unknown:216 (D)</option>
+      <option value="Unknown:216 (E)">Unknown:216 (E)</option>
+      <option value="Unknown:216 (N-term)">Unknown:216 (N-term)</option>
+      <option value="Unknown:234 (C-term)">Unknown:234 (C-term)</option>
+      <option value="Unknown:234 (D)">Unknown:234 (D)</option>
+      <option value="Unknown:234 (E)">Unknown:234 (E)</option>
+      <option value="Unknown:234 (N-term)">Unknown:234 (N-term)</option>
+      <option value="Unknown:248 (C-term)">Unknown:248 (C-term)</option>
+      <option value="Unknown:248 (D)">Unknown:248 (D)</option>
+      <option value="Unknown:248 (E)">Unknown:248 (E)</option>
+      <option value="Unknown:248 (N-term)">Unknown:248 (N-term)</option>
+      <option value="Unknown:250 (C-term)">Unknown:250 (C-term)</option>
+      <option value="Unknown:250 (D)">Unknown:250 (D)</option>
+      <option value="Unknown:250 (E)">Unknown:250 (E)</option>
+      <option value="Unknown:250 (N-term)">Unknown:250 (N-term)</option>
+      <option value="Unknown:302 (C-term)">Unknown:302 (C-term)</option>
+      <option value="Unknown:302 (D)">Unknown:302 (D)</option>
+      <option value="Unknown:302 (E)">Unknown:302 (E)</option>
+      <option value="Unknown:302 (N-term)">Unknown:302 (N-term)</option>
+      <option value="Unknown:306 (C-term)">Unknown:306 (C-term)</option>
+      <option value="Unknown:306 (D)">Unknown:306 (D)</option>
+      <option value="Unknown:306 (E)">Unknown:306 (E)</option>
+      <option value="Unknown:306 (N-term)">Unknown:306 (N-term)</option>
+      <option value="Unknown:420 (C-term)">Unknown:420 (C-term)</option>
+      <option value="Unknown:420 (N-term)">Unknown:420 (N-term)</option>
       <option value="Val-&gt;Ala (V)">Val-&gt;Ala (V)</option>
       <option value="Val-&gt;Arg (V)">Val-&gt;Arg (V)</option>
       <option value="Val-&gt;Asn (V)">Val-&gt;Asn (V)</option>
@@ -5338,38 +5916,99 @@
       <option value="Xle-&gt;Val (I)">Xle-&gt;Val (I)</option>
       <option value="Xle-&gt;Val (L)">Xle-&gt;Val (L)</option>
       <option value="Xlink:B10621 (C)">Xlink:B10621 (C)</option>
-      <option value="Xlink:DMP (K)">Xlink:DMP (K)</option>
-      <option value="Xlink:DMP (Protein N-term)">Xlink:DMP (Protein N-term)</option>
-      <option value="Xlink:DMP-de (K)">Xlink:DMP-de (K)</option>
-      <option value="Xlink:DMP-de (Protein N-term)">Xlink:DMP-de (Protein N-term)</option>
-      <option value="Xlink:DMP-s (K)">Xlink:DMP-s (K)</option>
-      <option value="Xlink:DMP-s (Protein N-term)">Xlink:DMP-s (Protein N-term)</option>
-      <option value="Xlink:DSS (K)">Xlink:DSS (K)</option>
-      <option value="Xlink:DSS (Protein N-term)">Xlink:DSS (Protein N-term)</option>
-      <option value="Xlink:DSS-NH2 (K)">Xlink:DSS-NH2 (K)</option>
-      <option value="Xlink:DSS-NH2 (Protein N-term)">Xlink:DSS-NH2 (Protein N-term)</option>
-      <option value="Xlink:DST (K)">Xlink:DST (K)</option>
-      <option value="Xlink:DST (Protein N-term)">Xlink:DST (Protein N-term)</option>
-      <option value="Xlink:DTSSP (K)">Xlink:DTSSP (K)</option>
-      <option value="Xlink:DTSSP (Protein N-term)">Xlink:DTSSP (Protein N-term)</option>
-      <option value="Xlink:EGS (K)">Xlink:EGS (K)</option>
-      <option value="Xlink:EGS (Protein N-term)">Xlink:EGS (Protein N-term)</option>
-      <option value="Xlink:EGScleaved (K)">Xlink:EGScleaved (K)</option>
-      <option value="Xlink:EGScleaved (Protein N-term)">Xlink:EGScleaved (Protein N-term)</option>
-      <option value="Xlink:SMCC (C)">Xlink:SMCC (C)</option>
-      <option value="Xlink:SSD (K)">Xlink:SSD (K)</option>
+      <option value="Xlink:BMOE (C)">Xlink:BMOE (C)</option>
+      <option value="Xlink:BS2G[113] (K)">Xlink:BS2G[113] (K)</option>
+      <option value="Xlink:BS2G[113] (Protein N-term)">Xlink:BS2G[113] (Protein N-term)</option>
+      <option value="Xlink:BS2G[114] (K)">Xlink:BS2G[114] (K)</option>
+      <option value="Xlink:BS2G[114] (Protein N-term)">Xlink:BS2G[114] (Protein N-term)</option>
+      <option value="Xlink:BS2G[217] (K)">Xlink:BS2G[217] (K)</option>
+      <option value="Xlink:BS2G[217] (Protein N-term)">Xlink:BS2G[217] (Protein N-term)</option>
+      <option value="Xlink:BS2G[96] (K)">Xlink:BS2G[96] (K)</option>
+      <option value="Xlink:BS2G[96] (Protein N-term)">Xlink:BS2G[96] (Protein N-term)</option>
+      <option value="Xlink:BuUrBu[111] (K)">Xlink:BuUrBu[111] (K)</option>
+      <option value="Xlink:BuUrBu[111] (Protein N-term)">Xlink:BuUrBu[111] (Protein N-term)</option>
+      <option value="Xlink:BuUrBu[196] (K)">Xlink:BuUrBu[196] (K)</option>
+      <option value="Xlink:BuUrBu[196] (Protein N-term)">Xlink:BuUrBu[196] (Protein N-term)</option>
+      <option value="Xlink:BuUrBu[213] (K)">Xlink:BuUrBu[213] (K)</option>
+      <option value="Xlink:BuUrBu[213] (Protein N-term)">Xlink:BuUrBu[213] (Protein N-term)</option>
+      <option value="Xlink:BuUrBu[214] (K)">Xlink:BuUrBu[214] (K)</option>
+      <option value="Xlink:BuUrBu[214] (Protein N-term)">Xlink:BuUrBu[214] (Protein N-term)</option>
+      <option value="Xlink:BuUrBu[317] (K)">Xlink:BuUrBu[317] (K)</option>
+      <option value="Xlink:BuUrBu[317] (Protein N-term)">Xlink:BuUrBu[317] (Protein N-term)</option>
+      <option value="Xlink:BuUrBu[85] (K)">Xlink:BuUrBu[85] (K)</option>
+      <option value="Xlink:BuUrBu[85] (Protein N-term)">Xlink:BuUrBu[85] (Protein N-term)</option>
+      <option value="Xlink:DFDNB (K)">Xlink:DFDNB (K)</option>
+      <option value="Xlink:DFDNB (N)">Xlink:DFDNB (N)</option>
+      <option value="Xlink:DFDNB (Q)">Xlink:DFDNB (Q)</option>
+      <option value="Xlink:DFDNB (R)">Xlink:DFDNB (R)</option>
+      <option value="Xlink:DMP[122] (K)">Xlink:DMP[122] (K)</option>
+      <option value="Xlink:DMP[122] (Protein N-term)">Xlink:DMP[122] (Protein N-term)</option>
+      <option value="Xlink:DMP[139] (K)">Xlink:DMP[139] (K)</option>
+      <option value="Xlink:DMP[139] (Protein N-term)">Xlink:DMP[139] (Protein N-term)</option>
+      <option value="Xlink:DMP[140] (K)">Xlink:DMP[140] (K)</option>
+      <option value="Xlink:DMP[140] (Protein N-term)">Xlink:DMP[140] (Protein N-term)</option>
+      <option value="Xlink:DMP[154] (K)">Xlink:DMP[154] (K)</option>
+      <option value="Xlink:DMP[154] (Protein N-term)">Xlink:DMP[154] (Protein N-term)</option>
+      <option value="Xlink:DSS[138] (K)">Xlink:DSS[138] (K)</option>
+      <option value="Xlink:DSS[138] (Protein N-term)">Xlink:DSS[138] (Protein N-term)</option>
+      <option value="Xlink:DSS[155] (K)">Xlink:DSS[155] (K)</option>
+      <option value="Xlink:DSS[155] (Protein N-term)">Xlink:DSS[155] (Protein N-term)</option>
+      <option value="Xlink:DSS[156] (K)">Xlink:DSS[156] (K)</option>
+      <option value="Xlink:DSS[156] (Protein N-term)">Xlink:DSS[156] (Protein N-term)</option>
+      <option value="Xlink:DSS[259] (K)">Xlink:DSS[259] (K)</option>
+      <option value="Xlink:DSS[259] (Protein N-term)">Xlink:DSS[259] (Protein N-term)</option>
+      <option value="Xlink:DSSO[104] (K)">Xlink:DSSO[104] (K)</option>
+      <option value="Xlink:DSSO[104] (Protein N-term)">Xlink:DSSO[104] (Protein N-term)</option>
+      <option value="Xlink:DSSO[158] (K)">Xlink:DSSO[158] (K)</option>
+      <option value="Xlink:DSSO[158] (Protein N-term)">Xlink:DSSO[158] (Protein N-term)</option>
+      <option value="Xlink:DSSO[175] (K)">Xlink:DSSO[175] (K)</option>
+      <option value="Xlink:DSSO[175] (Protein N-term)">Xlink:DSSO[175] (Protein N-term)</option>
+      <option value="Xlink:DSSO[176] (K)">Xlink:DSSO[176] (K)</option>
+      <option value="Xlink:DSSO[176] (Protein N-term)">Xlink:DSSO[176] (Protein N-term)</option>
+      <option value="Xlink:DSSO[279] (K)">Xlink:DSSO[279] (K)</option>
+      <option value="Xlink:DSSO[279] (Protein N-term)">Xlink:DSSO[279] (Protein N-term)</option>
+      <option value="Xlink:DSSO[54] (K)">Xlink:DSSO[54] (K)</option>
+      <option value="Xlink:DSSO[54] (Protein N-term)">Xlink:DSSO[54] (Protein N-term)</option>
+      <option value="Xlink:DSSO[86] (K)">Xlink:DSSO[86] (K)</option>
+      <option value="Xlink:DSSO[86] (Protein N-term)">Xlink:DSSO[86] (Protein N-term)</option>
+      <option value="Xlink:DST[114] (K)">Xlink:DST[114] (K)</option>
+      <option value="Xlink:DST[114] (Protein N-term)">Xlink:DST[114] (Protein N-term)</option>
+      <option value="Xlink:DST[132] (K)">Xlink:DST[132] (K)</option>
+      <option value="Xlink:DST[132] (Protein N-term)">Xlink:DST[132] (Protein N-term)</option>
+      <option value="Xlink:DST[56] (K)">Xlink:DST[56] (K)</option>
+      <option value="Xlink:DST[56] (Protein N-term)">Xlink:DST[56] (Protein N-term)</option>
+      <option value="Xlink:DTBP[172] (K)">Xlink:DTBP[172] (K)</option>
+      <option value="Xlink:DTBP[172] (Protein N-term)">Xlink:DTBP[172] (Protein N-term)</option>
+      <option value="Xlink:DTBP[87] (K)">Xlink:DTBP[87] (K)</option>
+      <option value="Xlink:DTBP[87] (Protein N-term)">Xlink:DTBP[87] (Protein N-term)</option>
+      <option value="Xlink:DTSSP[174] (K)">Xlink:DTSSP[174] (K)</option>
+      <option value="Xlink:DTSSP[174] (Protein N-term)">Xlink:DTSSP[174] (Protein N-term)</option>
+      <option value="Xlink:DTSSP[192] (K)">Xlink:DTSSP[192] (K)</option>
+      <option value="Xlink:DTSSP[192] (Protein N-term)">Xlink:DTSSP[192] (Protein N-term)</option>
+      <option value="Xlink:DTSSP[88] (K)">Xlink:DTSSP[88] (K)</option>
+      <option value="Xlink:DTSSP[88] (Protein N-term)">Xlink:DTSSP[88] (Protein N-term)</option>
+      <option value="Xlink:EGS[115] (K)">Xlink:EGS[115] (K)</option>
+      <option value="Xlink:EGS[115] (Protein N-term)">Xlink:EGS[115] (Protein N-term)</option>
+      <option value="Xlink:EGS[226] (K)">Xlink:EGS[226] (K)</option>
+      <option value="Xlink:EGS[226] (Protein N-term)">Xlink:EGS[226] (Protein N-term)</option>
+      <option value="Xlink:EGS[244] (K)">Xlink:EGS[244] (K)</option>
+      <option value="Xlink:EGS[244] (Protein N-term)">Xlink:EGS[244] (Protein N-term)</option>
+      <option value="Xlink:SMCC[219] (C)">Xlink:SMCC[219] (C)</option>
+      <option value="Xlink:SMCC[219] (K)">Xlink:SMCC[219] (K)</option>
+      <option value="Xlink:SMCC[219] (Protein N-term)">Xlink:SMCC[219] (Protein N-term)</option>
+      <option value="Xlink:SMCC[237] (C)">Xlink:SMCC[237] (C)</option>
+      <option value="Xlink:SMCC[237] (K)">Xlink:SMCC[237] (K)</option>
+      <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
+      <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
       <option value="ZGB (K)">ZGB (K)</option>
       <option value="ZGB (N-term)">ZGB (N-term)</option>
+      <option value="ZQG (K)">ZQG (K)</option>
       <expand macro="list_string_san"/>
     </param>
+    <param name="binary_modifications" argument="-binary_modifications" type="text" optional="true" value="" label="List of modification group indices" help="Indices correspond to the binary modification index used by comet to group individually searched lists of variable modifications.. Note: if set, both variable_modifications and binary_modifications need to have the same number of entries as the N-th entry corresponds to the N-th variable_modification..       if left empty (default), all entries are internally set to 0 generating all permutations of modified and unmodified residues..       For a detailed explanation please see the parameter description in the Comet help (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <expand macro="list_integer_valsan"/>
+    </param>
     <expand macro="adv_opts_macro">
-      <param name="fragment_bin_tolerance" argument="-fragment_bin_tolerance" type="float" optional="true" min="0.01" value="0.02" label="Bin size (in Da) for matching fragment ions" help="Ion trap: 1.0005, high res: 0.02. CAUTION: Low tolerances have heavy impact on RAM usage. Consider using use_sparse_matrix and/or spectrum_batch_size"/>
-      <param name="fragment_bin_offset" argument="-fragment_bin_offset" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Offset of fragment bins scaled by tolerance" help="Ion trap: 0.4, high res: 0.0"/>
-      <param name="instrument" argument="-instrument" display="radio" type="select" optional="false" label="Comets theoretical_fragment_ions parameter: theoretical fragment ion peak representation, high res ms/ms: sum of intensities plus flanking bins, ion trap (low_res) ms/ms: sum of intensities of central M bin only" help="">
-        <option value="low_res">low_res</option>
-        <option value="high_res" selected="true">high_res</option>
-        <expand macro="list_string_san"/>
-      </param>
       <param name="use_A_ions" argument="-use_A_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use A ions for PSM" help=""/>
       <param name="use_B_ions" argument="-use_B_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="use B ions for PSM" help=""/>
       <param name="use_C_ions" argument="-use_C_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use C ions for PSM" help=""/>
@@ -5377,6 +6016,21 @@
       <param name="use_Y_ions" argument="-use_Y_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="use Y ions for PSM" help=""/>
       <param name="use_Z_ions" argument="-use_Z_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use Z ions for PSM" help=""/>
       <param name="use_NL_ions" argument="-use_NL_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use neutral loss (NH3, H2O) ions from b/y for PSM" help=""/>
+      <param name="second_enzyme" argument="-second_enzyme" type="select" optional="true" label="Additional enzyme used for peptide digestion" help="">
+        <option value="">default (nothing chosen)</option>
+        <option value="Arg-C">Arg-C</option>
+        <option value="Asp-N">Asp-N</option>
+        <option value="Trypsin">Trypsin</option>
+        <option value="unspecific cleavage">unspecific cleavage</option>
+        <option value="Chymotrypsin">Chymotrypsin</option>
+        <option value="CNBr">CNBr</option>
+        <option value="Lys-C">Lys-C</option>
+        <option value="Lys-N">Lys-N</option>
+        <option value="PepsinA">PepsinA</option>
+        <option value="Trypsin/P">Trypsin/P</option>
+        <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+        <expand macro="list_string_san"/>
+      </param>
       <param name="digest_mass_range" argument="-digest_mass_range" type="text" optional="true" value="600:5000" label="MH+ peptide mass range to analyze" help="">
         <expand macro="list_string_san"/>
       </param>
@@ -5400,13 +6054,13 @@
       </param>
       <param name="max_variable_mods_in_peptide" argument="-max_variable_mods_in_peptide" type="integer" optional="true" value="5" label="Set a maximum number of variable modifications per peptide" help=""/>
       <param name="require_variable_mod" argument="-require_variable_mod" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, requires at least one variable modification per peptide" help=""/>
-      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
+      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
       <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
         <expand macro="list_string_san"/>
       </param>
     </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
-      <option value="pin_out_FLAG">pin_out (Enables the test mode (needed for internal use only))</option>
+    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="pin_out_FLAG">pin_out (Output file - for Percolator input)</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
@@ -5426,6 +6080,6 @@
   <help><![CDATA[Annotates MS/MS spectra using Comet.
 
 
-For more information, visit http://www.openms.de/documentation/TOPP_CometAdapter.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_CometAdapter.html]]></help>
   <expand macro="references"/>
 </tool>
--- a/filetypes.txt	Wed Sep 23 13:43:34 2020 +0000
+++ b/filetypes.txt	Tue Oct 13 19:10:16 2020 +0000
@@ -53,7 +53,7 @@
 paramXML      paramxml
 fasta         peff
 peplist       peplist
-# TODO pep.xml should be removed with OMS 2.6 https://github.com/OpenMS/OpenMS/pull/4541
+# TODO pep.xml should be removed with OMS 2.6 https://github.com/OpenMS/OpenMS/pull/4541 .. but still in the tests
 pep.xml       pepxml
 pepXML        pepxml
 png           png
--- a/generate-foo.sh	Wed Sep 23 13:43:34 2020 +0000
+++ b/generate-foo.sh	Tue Oct 13 19:10:16 2020 +0000
@@ -2,125 +2,126 @@
 
 # parse test definitions from OpenMS sources for a tool with a given id
 function get_tests2 {
-	id=$1
-	>&2 echo "generate tests for $id"
-	echo '<xml name="autotest_'"$id"'">'
+    id=$1
+    >&2 echo "generate tests for $id"
+    echo '<xml name="autotest_'"$id"'">'
 
-	# get the tests from the CMakeLists.txt
-	# 1st remove some tests
-	# - Filefilter with empty select_palarity value (empty is not in the list of allowed options)
-	# - MassTraceExtractor with outdated ini file leading to wrong parameters https://github.com/OpenMS/OpenMS/issues/4386
-	# - OpenSwathMzMLFileCacher with -convert_back argumen https://github.com/OpenMS/OpenMS/issues/4399
+    # get the tests from the CMakeLists.txt
+    # 1st remove some tests
+    # - OpenSwathMzMLFileCacher with -convert_back argumen https://github.com/OpenMS/OpenMS/issues/4399
     # - IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differentlt
-	# - several tools with duplicated input (leads to conflict when linking)
-	# - TOFCalibration inputs we extension (also in prepare_test_data) https://github.com/OpenMS/OpenMS/pull/4525
-	# - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456)
-	# - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed)
-	# - some input files are originally in a subdir (degenerated cases/), but not in test-data
-	# - SeedListGenerator: https://github.com/OpenMS/OpenMS/issues/4404
-	# - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet)
-	CMAKE=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake  |
-		sed 's@${DATA_DIR_SHARE}/@@g' |
-		grep -v 'OpenSwathMzMLFileCacher .*-convert_back' |
-	    	sed 's/${TMP_RIP_PATH}/""/' |
-		sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @' |
-		grep -v "MaRaClusterAdapter.*-consensus_out"|
- 		grep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " |
-		sed 's@degenerate_cases/@@g' |
-		grep -v 'TOPP_SeedListGenerator_3"' | 
-		egrep -v 'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"')
+    # - several tools with duplicated input (leads to conflict when linking)
+    # - TOFCalibration inputs we extension (also in prepare_test_data) https://github.com/OpenMS/OpenMS/pull/4525
+    # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456)
+    # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed)
+    # - some input files are originally in a subdir (degenerated cases/), but not in test-data
+    # - SeedListGenerator: https://github.com/OpenMS/OpenMS/issues/4404
+    # - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet)
+    # - FeatureFinderIdentification name clash of two tests https://github.com/OpenMS/OpenMS/pull/5002
+    # - TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010
+    CMAKE=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake  |
+        sed 's@${DATA_DIR_SHARE}/@@g' |
+        grep -v 'OpenSwathMzMLFileCacher .*-convert_back' |
+        sed 's/${TMP_RIP_PATH}/""/' |
+        grep -v "MaRaClusterAdapter.*-consensus_out"|
+        grep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " |
+        sed 's@degenerate_cases/@@g' |
+        grep -v 'TOPP_SeedListGenerator_3"' | 
+        egrep -v 'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"' |
+	egrep -v '"TOPP_FeatureFinderIdentification_4"' | 
+	sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/')
 
 
-# 		grep -v 'FileFilter.*-spectra:select_polarity ""' |
-# 		grep -v 'MassTraceExtractor_2.ini ' |
-# 		grep -v "FileMerger_6_input2.mzML.*FileMerger_6_input2.mzML" |
-# 		grep -v "IDMerger_1_input1.idXML.*IDMerger_1_input1.idXML" |
-# 		grep -v "degenerated_empty.idXML.*degenerated_empty.idXML" |
-# 		grep -v "FeatureLinkerUnlabeledKD_1_output.consensusXML.*FeatureLinkerUnlabeledKD_1_output.consensusXML" |
-# 		grep -v "FeatureLinkerUnlabeledQT_1_output.consensusXML.*FeatureLinkerUnlabeledQT_1_output.consensusXML" |
+#         grep -v 'FileFilter.*-spectra:select_polarity ""' |
+#         grep -v 'MassTraceExtractor_2.ini ' |
+#         grep -v "FileMerger_6_input2.mzML.*FileMerger_6_input2.mzML" |
+#         grep -v "IDMerger_1_input1.idXML.*IDMerger_1_input1.idXML" |
+#         grep -v "degenerated_empty.idXML.*degenerated_empty.idXML" |
+#         grep -v "FeatureLinkerUnlabeledKD_1_output.consensusXML.*FeatureLinkerUnlabeledKD_1_output.consensusXML" |
+#         grep -v "FeatureLinkerUnlabeledQT_1_output.consensusXML.*FeatureLinkerUnlabeledQT_1_output.consensusXML" |
 
-	# 1st part is a dirty hack to join lines containing a single function call, e.g.
-	# addtest(....
-	#         ....)
-	echo "$CMAKE" | sed 's/#.*//; s/^\s*//; s/\s*$//' | grep -v "^#" | grep -v "^$"  | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | 
-		grep -iE "add_test\(\"(TOPP|UTILS)_.*/$id " | egrep -v "_prepare\"|_convert|WRITEINI|WRITECTD|INVALIDVALUE"  | while read -r line
-	do
-		line=$(echo "$line" | sed 's/add_test("\([^"]\+\)"/\1/; s/)$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g')
-		# >&2 echo $line
-		test_id=$(echo "$line" | cut -d" " -f 1)
-		tool_id=$(echo "$line" | cut -d" " -f 2)
-		if [[ $test_id =~ _out_?[0-9]? ]]; then
-			>&2 echo "    skip $test_id $line"
-			continue
-		fi
-		if [[ ${id,,} != ${tool_id,,} ]]; then
-			>&2 echo "    skip $test_id ($id != $tool_id) $line"
-			continue
-		fi
+    # 1st part is a dirty hack to join lines containing a single function call, e.g.
+    # addtest(....
+    #         ....)
+    echo "$CMAKE" | sed 's/#.*//; s/^\s*//; s/\s*$//' | grep -v "^#" | grep -v "^$"  | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | 
+        grep -iE "add_test\(\"(TOPP|UTILS)_.*/$id " | egrep -v "_prepare\"|_convert|WRITEINI|WRITECTD|INVALIDVALUE"  | while read -r line
+    do
+        line=$(echo "$line" | sed 's/add_test("\([^"]\+\)"/\1/; s/)$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g')
+        # >&2 echo $line
+        test_id=$(echo "$line" | cut -d" " -f 1)
+        tool_id=$(echo "$line" | cut -d" " -f 2)
+        if [[ $test_id =~ _out_?[0-9]? ]]; then
+            >&2 echo "    skip $test_id $line"
+            continue
+        fi
+        if [[ ${id,,} != ${tool_id,,} ]]; then
+            >&2 echo "    skip $test_id ($id != $tool_id) $line"
+            continue
+        fi
 
-		#remove tests with set_tests_properties(....PROPERTIES WILL_FAIL 1)
-		if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then
-			>&2 echo "    skip failing "$test_id
-			continue
-		fi
-		tes="  <test>\n"
-		line=$(fix_tmp_files "$line")
-		line=$(unique_files "$line")
-		# >&2 echo $line
-		#if there is an ini file then we use this to generate the test
-		#otherwise the ctd file is used
-		#other command line parameters are inserted later into this xml
-		if grep -lq "\-ini" <<<"$line"; then
-			ini=$(echo $line | sed 's/.*-ini \([^ ]\+\).*/\1/')
-			ini="test-data/$ini"
-		else
-			ini="ctd/$tool_id.ctd"
-		fi
-		cli=$(echo $line |cut -d" " -f3- | sed 's/-ini [^ ]\+//')
-		
-		ctdtmp=$(mktemp)
-		#echo python3 fill_ctd_clargs.py --ctd $ini $cli
-		# using eval: otherwise for some reason quoted values are not used properly ('A B' -> ["'A", "B'"])
-		# >&2 echo "python3 fill_ctd_clargs.py --ctd $ini $cli"
-		eval "python3 fill_ctd_clargs.py --ctd $ini $cli" > "$ctdtmp"
-		# echo $ctdtmp
- 		# >&2 cat $ctdtmp
-  		testtmp=$(mktemp)
- 		python3 $CTDCONVERTER/convert.py galaxy -i $ctdtmp -o $testtmp -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf  -p hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib > /dev/null
-	   	cat $testtmp | grep -v '<output.*file=""' # | grep -v 'CHEMISTRY/'
-		rm $ctdtmp $testtmp
+        #remove tests with set_tests_properties(....PROPERTIES WILL_FAIL 1)
+        if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then
+            >&2 echo "    skip failing "$test_id
+            continue
+        fi
+        tes="  <test>\n"
+        line=$(fix_tmp_files "$line")
+        line=$(unique_files "$line")
+        # >&2 echo $line
+        #if there is an ini file then we use this to generate the test
+        #otherwise the ctd file is used
+        #other command line parameters are inserted later into this xml
+        if grep -lq "\-ini" <<<"$line"; then
+            ini=$(echo $line | sed 's/.*-ini \([^ ]\+\).*/\1/')
+            ini="test-data/$ini"
+        else
+            ini="ctd/$tool_id.ctd"
+        fi
+        cli=$(echo $line |cut -d" " -f3- | sed 's/-ini [^ ]\+//')
 
-		#> /dev/null
+        ctdtmp=$(mktemp)
+        #echo python3 fill_ctd_clargs.py --ctd $ini $cli
+        # using eval: otherwise for some reason quoted values are not used properly ('A B' -> ["'A", "B'"])
+        # >&2 echo "python3 fill_ctd_clargs.py --ctd $ini $cli"
+        eval "python3 fill_ctd_clargs.py --ctd $ini $cli" > "$ctdtmp"
+        # echo $ctdtmp
+        # >&2 cat $ctdtmp
+        testtmp=$(mktemp)
+        python3 $CTDCONVERTER/convert.py galaxy -i $ctdtmp -o $testtmp -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf  -p hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib > /dev/null
+        cat $testtmp | grep -v '<output.*file=""' # | grep -v 'CHEMISTRY/'
+        rm $ctdtmp $testtmp
 
-		#rm $testtmp
-	done 
-	echo '</xml>'
+        #> /dev/null
+
+        #rm $testtmp
+    done 
+    echo '</xml>'
 }
 
 #some tests use the same file twice which does not work in planemo tests
 #hence we create symlinks for each file used twice
 function unique_files {
-	line=$@
-	for arg in $@
-	do
-		if [[ ! -f "test-data/$arg" ]]; then
-			continue
-		fi
-		cnt=$(grep -c $arg <<< $(echo "$line" | tr ' ' '\n'))
-		while [[ $cnt -gt 1 ]]; do
+    line=$@
+    for arg in $@
+    do
+        if [[ ! -f "test-data/$arg" ]]; then
+            continue
+        fi
+        cnt=$(grep -c $arg <<< $(echo "$line" | tr ' ' '\n'))
+        while [[ $cnt -gt 1 ]]; do
             new_arg=$(echo $arg | sed "s/\(.*\)\./\1_$cnt./")
-			ln -fs $arg test-data/$new_arg
-			line=$(echo $line | sed "s/\($arg.*\)$arg/\1$new_arg/")
-			cnt=$(grep -c $arg <<< $(echo "$line" | tr ' ' '\n'))
-		done
-	done
+            ln -fs $arg test-data/$new_arg
+            line=$(echo $line | sed "s/\($arg.*\)$arg/\1$new_arg/")
+            cnt=$(grep -c $arg <<< $(echo "$line" | tr ' ' '\n'))
+        done
+    done
 
-	echo $line
+    echo $line
 }
 
 # options of out_type selects need to be fixed to Galaxy data types
 function fix_out_type {
-	grep "^$1" "$2" | awk '{print $2}'
+    grep "^$1" "$2" | awk '{print $2}'
 }
 
 #OpenMS tests output to tmp files and compare with FuzzyDiff to the expected file.
@@ -129,34 +130,34 @@
 #(e.g. for prepare_test_data, e.g. CLI expects csv but test file is txt)
 #this function replaces the tmp file by the expected file. 
 function fix_tmp_files {
-#	>&2 echo "FIX $line"
-	ret=""
-	for a in $@; do
-		if [[ ! $a =~ .tmp$ ]]; then
-			ret="$ret $a"
-			continue
-		fi
-#		>&2 echo "    a "$a
-		g=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep '\${DIFF}.*'"$a")
-#		>&2 echo "    g "$g
-		in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$g)
-		# >&2 echo "    in1 "$in1
-		if [[  "$a" != "$in1" ]]; then
-			ret="$ret $a"
-			continue
-		fi
-		in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$g)
-		in2=$(basename $in2 | sed 's/)$//')
-		# >&2 echo "    in2 "$in2
-		if [[ -f "test-data/$in2" ]]; then
-			ln -fs "$in1" "test-data/$in2"
-			ret="$ret $in2"
-		else
-			ret="$ret $a"
-		fi
-	done
-#	>&2 echo "--> $ret"
-	echo "$ret"
+#    >&2 echo "FIX $line"
+    ret=""
+    for a in $@; do
+        if [[ ! $a =~ .tmp$ ]]; then
+            ret="$ret $a"
+            continue
+        fi
+#        >&2 echo "    a "$a
+        g=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep '\${DIFF}.*'"$a")
+#        >&2 echo "    g "$g
+        in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$g)
+        # >&2 echo "    in1 "$in1
+        if [[  "$a" != "$in1" ]]; then
+            ret="$ret $a"
+            continue
+        fi
+        in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$g)
+        in2=$(basename $in2 | sed 's/)$//')
+        # >&2 echo "    in2 "$in2
+        if [[ -f "test-data/$in2" ]]; then
+            ln -fs "$in1" "test-data/$in2"
+            ret="$ret $in2"
+        else
+            ret="$ret $a"
+        fi
+    done
+#    >&2 echo "--> $ret"
+    echo "$ret"
 }
 
 function link_tmp_files {
@@ -190,28 +191,32 @@
 
 # parse data preparation calls from OpenMS sources for a tool with a given id
 function prepare_test_data {
-# 	id=$1
+#     id=$1
 # | egrep -i "$id\_.*[0-9]+(_prepare\"|_convert)?"
-	cat $OPENMSGIT/src/tests/topp/CMakeLists.txt  $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's/#.*$//'| sed 's/^\s*//; s/\s*$//' | grep -v "^$"  | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | 
-		sed 's/degenerate_cases\///' | 
-		egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" | 
-		grep add_test | 
-		egrep "TOPP|UTILS" |
-		sed 's@${DATA_DIR_SHARE}/@@g;'|
-		sed 's@${TMP_RIP_PATH}@dummy2.tmp@g'|
-		sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @'| 
-	while read line
-	do
-		test_id=$(echo "$line" | sed 's/add_test(//; s/"//g;  s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f1)
 
-		if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then
-			>&2 echo "    skip failing "$test_id
-			continue
-		fi
+# TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010
+    cat $OPENMSGIT/src/tests/topp/CMakeLists.txt  $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's/#.*$//'| sed 's/^\s*//; s/\s*$//' | grep -v "^$"  | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | 
+        sed 's/degenerate_cases\///' | 
+        egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" | 
+        grep add_test | 
+        egrep "TOPP|UTILS" |
+        sed 's@${DATA_DIR_SHARE}/@@g;'|
+        sed 's@${TMP_RIP_PATH}@dummy2.tmp@g'|
+        sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @'| 
+	sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' |
+    while read line
+    do
+        test_id=$(echo "$line" | sed 's/add_test(//; s/"//g;  s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f1)
 
-		line=$(echo "$line" | sed 's/add_test("//; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f2-)
-		# line="$(fix_tmp_files $line)"
-		echo "$line > $test_id.stdout 2> $test_id.stderr"
-		echo "if [[ \"\$?\" -ne \"0\" ]]; then >&2 echo '$test_id failed'; >&2 echo -e \"stderr:\n\$(cat $test_id.stderr | sed 's/^/    /')\"; echo -e \"stdout:\n\$(cat $test_id.stdout)\";fi"	
+        if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then
+            >&2 echo "    skip failing "$test_id
+            continue
+        fi
+
+        line=$(echo "$line" | sed 's/add_test("//; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f2-)
+        # line="$(fix_tmp_files $line)"
+        echo 'echo executing "'$test_id'"'
+	echo "$line > $test_id.stdout 2> $test_id.stderr"
+        echo "if [[ \"\$?\" -ne \"0\" ]]; then >&2 echo '$test_id failed'; >&2 echo -e \"stderr:\n\$(cat $test_id.stderr | sed 's/^/    /')\"; echo -e \"stdout:\n\$(cat $test_id.stdout)\";fi"    
     done
 }
--- a/generate.sh	Wed Sep 23 13:43:34 2020 +0000
+++ b/generate.sh	Tue Oct 13 19:10:16 2020 +0000
@@ -1,20 +1,13 @@
 #!/usr/bin/env bash
 
-# VERSION=2.3
-# CONDAPKG=https://anaconda.org/bioconda/openms/2.3.0/download/linux-64/openms-2.3.0-py27h932d754_3.tar.bz2
-# VERSION=2.4
-# CONDAPKG=https://anaconda.org/bioconda/openms/2.4.0/download/linux-64/openms-2.4.0-py27h574aadf_1.tar.bz2
-
-VERSION=2.5
+VERSION=2.6
 FILETYPES="filetypes.txt"
 PROFILE="20.05"
 ## FILETYPES_RE=$(grep -v "^#" $FILETYPES | grep -v "^$" | cut -f 1 -d" " | tr '\n' '|' | sed 's/|$//'| sed 's/|/\\|/g')
 
 export tmp=$(mktemp -d)
-
 export CTDCONVERTER="$tmp/CTDConverter"
 
-export PYTHONPATH="$(pwd)/CTDopts/"
 ###############################################################################
 ## reset old data
 ###############################################################################
@@ -59,6 +52,8 @@
 ###############################################################################
 ## conversion ctd->xml 
 ###############################################################################
+
+find . -maxdepth 0 -name "[A-Z]*xml" -delete
 source $(dirname $(which conda))/../etc/profile.d/conda.sh
 conda activate $tmp/OpenMS$VERSION-env
 python $CTDCONVERTER/convert.py galaxy -i ctd/*ctd -o ./ -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf  -p hardcoded_params.json --test-macros macros_autotest.xml --test-macros-prefix autotest_  --test-macros macros_test.xml --test-macros-prefix manutest_ --tool-version $VERSION --tool-profile $PROFILE > convert.out 2> convert.err
@@ -67,6 +62,10 @@
 
 patch PepNovoAdapter.xml < PepNovoAdapter.patch
 patch OMSSAAdapter.xml < OMSSAAdapter.patch
+
+# https://github.com/OpenMS/OpenMS/pull/4984
+sed -i -e 's@http://www.openms.de/documentation/@http://www.openms.de/doxygen/release/2.6.0/html/@' ./*xml
+# https://github.com/OpenMS/OpenMS/pull/4984#issuecomment-702641976
 patch -p0 <404-urls.patch
 
 # #-b version log debug test in_type executable pepnovo_executable param_model_directory rt_concat_trafo_out param_id_pool
--- a/hardcoded_params.json	Wed Sep 23 13:43:34 2020 +0000
+++ b/hardcoded_params.json	Tue Oct 13 19:10:16 2020 +0000
@@ -119,6 +119,10 @@
 	"threads": [{
 		"value": "${GALAXY_SLOTS:-1}"
 	}],
+	"sirius:cores": [{
+		"value": "${GALAXY_SLOTS:-1}"
+	}],
+
 	"#": "hardcode the outer loop threads for OpenSwathWorkflow",
 	"outer_loop_threads": [{
 			"value": "1", 
@@ -128,6 +132,13 @@
 		"value": ",",
 		"tools": ["IDMassAccuracy"]
 	}],
+
+	"#": "don't alow to copy data internally to save computation time for reloading",
+	"copy_data": [{
+		"value": "false",
+		"tools": ["MapAlignerTreeGuided"]
+	}],
+
 	"#": "overwrite/add Galaxy xml attributes of some parameters (names need to start with param_)",
 
 	"#": "test is not a hardcoded value since we need to set it in the tool tests", 
@@ -146,8 +157,6 @@
 
 	"#": "SeedListGenerator with consensusXML input needs a dynamic number of outputs that depends on the content of the input, so we remove this options at the moment because its hard or impossible to implement in Galaxy, https://github.com/OpenMS/OpenMS/issues/4404 .. see also in parameter",
 	"#": "FileInfo, MapStatistics, SequenceCoverageCalculator wo -out just writes to stdout. not wanted here",
-	"#": "MascotAdapter: https://github.com/OpenMS/OpenMS/pull/4553",
-	"#": "Phosphoscoring: https://github.com/OpenMS/OpenMS/pull/4569",
 	"#": "MzMLSplitter output prefix https://github.com/OpenMS/OpenMS/issues/4404",
 	"#": "IDRipper: blacklist out (is doing the same as the output-prefix out-path)",
 	"out": [{
@@ -157,12 +166,6 @@
 	 	"CTD:required": true,
 		"tools": ["FileInfo", "MapStatistics", "SequenceCoverageCalculator"]
 	}, {
-		"CTD:restrictions": "idXML",
-		"tools": ["MascotAdapter"]
-	}, {
-		"CTD:restrictions": "idXML",
-		"tools": ["PhosphoScoring"]	
-	}, {
 		"CTD:type": "output-prefix", 
 		"CTD:required": true,
 		"CTD:restrictions": "mzml",
@@ -172,25 +175,8 @@
 		"tools": ["IDRipper"]
 	}],
 
-	"#": "https://github.com/OpenMS/OpenMS/pull/4552 .. if this is removed the test will need out_cm_FLAG",
-	"out_cm": [{
-		"CTD:required": true, 
-		"tools": ["MetaboliteAdductDecharger"]
-	}],
-
-
-	"#": "https://github.com/OpenMS/OpenMS/pull/4451", 
-	"out_xquestxml": [{
-		"CTD:restrictions": "xquest.xml",
-		"tools": ["OpenPepXL", "OpenPepXLLF"]
-	}],
-	"out_xquest_specxml": [{
-		"CTD:restrictions": "spec.xml",
-		"tools": ["OpenPepXL", "OpenPepXLLF"]
-	}],
-
 	"#": "Try to remove xml data type whereever possible",
-	"#": "XTandem Adapter output is called .xml in OMS -> use Galaxy's bioml",
+	"#": "XTandem Adapter output is called .xml in OMS which is to unspecific -> use Galaxy's bioml",
 	"xml_out": [{
 		"CTD:restrictions": "bioml",
 		"tools": ["XTandemAdapter"]
@@ -199,8 +185,7 @@
 	"#": "IDFileConverter remove xml",
 	"#": "OpenSwathWorkflow make in single file input and all outputs non-optional",
         "#": "XFDR does not need xml .. redundant with xquest.xml TODO check if list is up to date with each new release",
-        "#": "SpectraSTSearchAdapter does not need xml .. redundant with pep.xml TODO check if list is up to date with each new release",
-	"#": "SeedListGenerator https://github.com/OpenMS/OpenMS/issues/4404 .. see also out parameter",
+	"#": "SeedListGenerator: remove consensusXML https://github.com/OpenMS/OpenMS/issues/4404 .. see also out parameter",
 	"in": [{
 		"CTD:restrictions": "pepXML,protXML,mascotXML,omssaXML,bioml,psms,tsv,idXML,mzid,xquest.xml",
 		"tools": ["IDFileConverter"]
@@ -211,19 +196,10 @@
 		"CTD:restrictions": "idXML,mzid,xquest.xml",
 		"tools": ["XFDR"]
 	}, {
-		"CTD:restrictions": "txt,tsv,pep.xml,pepXML,html",
-		"tools": ["SpectraSTSearchAdapter"]
-	}, {
 		"CTD:restrictions": "mzML,idXML,featureXML",
 		"tools": ["SeedListGenerator"]
 	}],
 
-	"#": "parameter is a flag but restrictions in wrong order: TODO https://github.com/OpenMS/OpenMS/pull/4455",
-	"# masstrace_snr_filtering": [{
-		"CTD:restrictions": "true,false",
-		"tools": ["MassTraceExtractor"]
-	}],
-
 	"#": "IDMapper has in and spectra:in params, in is used in out as format_source",
 	"#": "which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493", 
 	"spectra:in": [{
@@ -231,6 +207,7 @@
 		"tools": ["IDMapper"]
 	}],
 
+	"#": "hardcoding prefix parameters which are not yet available in OMS but in CTDOpts https://github.com/OpenMS/OpenMS/pull/4527",
 	"#": "output-prefix",
 	"out_path": [{
 		"CTD:type": "output-prefix", 
@@ -244,5 +221,16 @@
 		"CTD:required": true,
 		"CTD:restrictions": "mzml",
 		"tools": ["OpenSwathFileSplitter"]
+	}],
+
+	"#": "OpenSwathDIAPreScoring: https://github.com/OpenMS/OpenMS/pull/4443",
+        "#": "SpectraSTSearchAdapter does not need xml .. redundant with pep.xml TODO check if list is up to date with each new release",
+	"output_files": [{
+		"CTD:required": true,
+		"tools": ["OpenSwathDIAPreScoring"]
+	}, {
+		"CTD:restrictions": "txt,tsv,pep.xml,pepXML,html",
+		"tools": ["SpectraSTSearchAdapter"]
+	
 	}]
 }
--- a/macros.xml	Wed Sep 23 13:43:34 2020 +0000
+++ b/macros.xml	Tue Oct 13 19:10:16 2020 +0000
@@ -3,7 +3,7 @@
      You can edit this file to add your own macros, if you so desire, or you can
      add additional macro files using the m/macros parameter -->
 <macros>
-  <token name="@TOOL_VERSION@">2.5</token>
+  <token name="@TOOL_VERSION@">2.6</token>
   <token name="@GALAXY_VERSION@">0</token>
   <xml name="requirements">
     <requirements>
@@ -11,7 +11,6 @@
       <requirement type="package" version="@TOOL_VERSION@">openms-thirdparty</requirement>
       <!-- makeblastdb for OMSSAAdapter -->
       <requirement type="package" version="2.9.0">blast</requirement>
-      <requirement type="package" version="8.0.192">openjdk</requirement>
       <!--<requirement type="package" version="5.0.0">tpp</requirement>-->
       <!-- for realpath (used e.g. in LuciphorAdapter) -->
 	  <!--<requirement type="package" version="8.25">coreutils</requirement>-->
--- a/macros_autotest.xml	Wed Sep 23 13:43:34 2020 +0000
+++ b/macros_autotest.xml	Tue Oct 13 19:10:16 2020 +0000
@@ -158,7 +158,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -228,7 +227,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -298,7 +296,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -368,7 +365,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -438,7 +434,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -508,7 +503,6 @@
         <param name="compound_timeout" value="100"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -578,7 +572,6 @@
         <param name="compound_timeout" value="100"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -648,7 +641,6 @@
         <param name="compound_timeout" value="100"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -718,7 +710,6 @@
         <param name="compound_timeout" value="100"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -760,9 +751,6 @@
     <test expect_num_outputs="3">
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
-        <param name="fragment_bin_tolerance" value="1.0005"/>
-        <param name="fragment_bin_offset" value="0.25"/>
-        <param name="instrument" value="high_res"/>
         <param name="use_A_ions" value="false"/>
         <param name="use_B_ions" value="true"/>
         <param name="use_C_ions" value="false"/>
@@ -770,6 +758,7 @@
         <param name="use_Y_ions" value="true"/>
         <param name="use_Z_ions" value="false"/>
         <param name="use_NL_ions" value="false"/>
+        <param name="second_enzyme" value=""/>
         <param name="digest_mass_range" value="600:5000"/>
         <param name="max_precursor_charge" value="5"/>
         <param name="spectrum_batch_size" value="1000"/>
@@ -781,7 +770,7 @@
         <param name="clear_mz_range" value="0:0"/>
         <param name="max_variable_mods_in_peptide" value="5"/>
         <param name="require_variable_mod" value="false"/>
-        <param name="force" value="false"/>
+        <param name="force" value="true"/>
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="spectra_comet.mzML"/>
@@ -791,9 +780,15 @@
       <param name="precursor_mass_tolerance" value="3.0"/>
       <param name="precursor_error_units" value="ppm"/>
       <param name="isotope_error" value="off"/>
+      <param name="fragment_mass_tolerance" value="0.50025"/>
+      <param name="fragment_error_units" value="Da"/>
+      <param name="fragment_bin_offset" value="0.25"/>
+      <param name="instrument" value="high_res"/>
       <param name="enzyme" value="Trypsin"/>
       <param name="num_enzyme_termini" value="fully"/>
-      <param name="allowed_missed_cleavages" value="1"/>
+      <param name="missed_cleavages" value="1"/>
+      <param name="min_peptide_length" value="5"/>
+      <param name="max_peptide_length" value="63"/>
       <param name="num_hits" value="5"/>
       <param name="precursor_charge" value="0:0"/>
       <param name="override_charge" value="keep any known"/>
@@ -803,6 +798,7 @@
       <param name="clip_nterm_methionine" value="false"/>
       <param name="fixed_modifications" value=""/>
       <param name="variable_modifications" value=""/>
+      <param name="binary_modifications" value=""/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
@@ -813,9 +809,6 @@
     <test expect_num_outputs="3">
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
-        <param name="fragment_bin_tolerance" value="1.0005"/>
-        <param name="fragment_bin_offset" value="0.25"/>
-        <param name="instrument" value="high_res"/>
         <param name="use_A_ions" value="false"/>
         <param name="use_B_ions" value="true"/>
         <param name="use_C_ions" value="false"/>
@@ -823,6 +816,7 @@
         <param name="use_Y_ions" value="true"/>
         <param name="use_Z_ions" value="false"/>
         <param name="use_NL_ions" value="false"/>
+        <param name="second_enzyme" value=""/>
         <param name="digest_mass_range" value="600:5000"/>
         <param name="max_precursor_charge" value="5"/>
         <param name="spectrum_batch_size" value="1000"/>
@@ -834,7 +828,7 @@
         <param name="clear_mz_range" value="0:0"/>
         <param name="max_variable_mods_in_peptide" value="5"/>
         <param name="require_variable_mod" value="false"/>
-        <param name="force" value="false"/>
+        <param name="force" value="true"/>
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="CometAdapter_2_prepared.mzML"/>
@@ -844,9 +838,15 @@
       <param name="precursor_mass_tolerance" value="3.0"/>
       <param name="precursor_error_units" value="Da"/>
       <param name="isotope_error" value="off"/>
+      <param name="fragment_mass_tolerance" value="0.50025"/>
+      <param name="fragment_error_units" value="Da"/>
+      <param name="fragment_bin_offset" value="0.25"/>
+      <param name="instrument" value="high_res"/>
       <param name="enzyme" value="Trypsin"/>
       <param name="num_enzyme_termini" value="fully"/>
-      <param name="allowed_missed_cleavages" value="1"/>
+      <param name="missed_cleavages" value="1"/>
+      <param name="min_peptide_length" value="5"/>
+      <param name="max_peptide_length" value="63"/>
       <param name="num_hits" value="5"/>
       <param name="precursor_charge" value="0:0"/>
       <param name="override_charge" value="keep any known"/>
@@ -856,6 +856,7 @@
       <param name="clip_nterm_methionine" value="false"/>
       <param name="fixed_modifications" value=""/>
       <param name="variable_modifications" value=""/>
+      <param name="binary_modifications" value=""/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
@@ -866,9 +867,6 @@
     <test expect_num_outputs="3">
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
-        <param name="fragment_bin_tolerance" value="0.02"/>
-        <param name="fragment_bin_offset" value="0.0"/>
-        <param name="instrument" value="high_res"/>
         <param name="use_A_ions" value="false"/>
         <param name="use_B_ions" value="true"/>
         <param name="use_C_ions" value="false"/>
@@ -876,6 +874,7 @@
         <param name="use_Y_ions" value="true"/>
         <param name="use_Z_ions" value="false"/>
         <param name="use_NL_ions" value="false"/>
+        <param name="second_enzyme" value=""/>
         <param name="digest_mass_range" value="600:5000"/>
         <param name="max_precursor_charge" value="5"/>
         <param name="spectrum_batch_size" value="20000"/>
@@ -897,9 +896,15 @@
       <param name="precursor_mass_tolerance" value="5.0"/>
       <param name="precursor_error_units" value="ppm"/>
       <param name="isotope_error" value="off"/>
+      <param name="fragment_mass_tolerance" value="0.01"/>
+      <param name="fragment_error_units" value="Da"/>
+      <param name="fragment_bin_offset" value="0.0"/>
+      <param name="instrument" value="high_res"/>
       <param name="enzyme" value="Trypsin"/>
       <param name="num_enzyme_termini" value="fully"/>
-      <param name="allowed_missed_cleavages" value="3"/>
+      <param name="missed_cleavages" value="3"/>
+      <param name="min_peptide_length" value="5"/>
+      <param name="max_peptide_length" value="63"/>
       <param name="num_hits" value="5"/>
       <param name="precursor_charge" value="0:0"/>
       <param name="override_charge" value="keep known search unknown"/>
@@ -909,6 +914,7 @@
       <param name="clip_nterm_methionine" value="false"/>
       <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
       <param name="variable_modifications" value="Acetyl (Protein N-term),Carbamidomethyl (N-term)"/>
+      <param name="binary_modifications" value=""/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
@@ -916,6 +922,63 @@
         </assert_contents>
       </output>
     </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="use_A_ions" value="false"/>
+        <param name="use_B_ions" value="true"/>
+        <param name="use_C_ions" value="false"/>
+        <param name="use_X_ions" value="false"/>
+        <param name="use_Y_ions" value="true"/>
+        <param name="use_Z_ions" value="false"/>
+        <param name="use_NL_ions" value="false"/>
+        <param name="second_enzyme" value=""/>
+        <param name="digest_mass_range" value="600:1200"/>
+        <param name="max_precursor_charge" value="5"/>
+        <param name="spectrum_batch_size" value="20000"/>
+        <param name="mass_offsets" value="0.0"/>
+        <param name="minimum_peaks" value="10"/>
+        <param name="minimum_intensity" value="0.0"/>
+        <param name="remove_precursor_peak" value="no"/>
+        <param name="remove_precursor_tolerance" value="1.5"/>
+        <param name="clear_mz_range" value="0:0"/>
+        <param name="max_variable_mods_in_peptide" value="3"/>
+        <param name="require_variable_mod" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="examples/FRACTIONS/BSA1_F1.mzML"/>
+      <output name="out" file="CometAdapter_4_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="database" value="examples/TOPPAS/data/BSA_Identification/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta"/>
+      <param name="precursor_mass_tolerance" value="5.0"/>
+      <param name="precursor_error_units" value="ppm"/>
+      <param name="isotope_error" value="off"/>
+      <param name="fragment_mass_tolerance" value="0.01"/>
+      <param name="fragment_error_units" value="Da"/>
+      <param name="fragment_bin_offset" value="0.0"/>
+      <param name="instrument" value="high_res"/>
+      <param name="enzyme" value="Trypsin"/>
+      <param name="num_enzyme_termini" value="fully"/>
+      <param name="missed_cleavages" value="3"/>
+      <param name="min_peptide_length" value="5"/>
+      <param name="max_peptide_length" value="63"/>
+      <param name="num_hits" value="5"/>
+      <param name="precursor_charge" value="0:0"/>
+      <param name="override_charge" value="keep known search unknown"/>
+      <param name="ms_level" value="2"/>
+      <param name="activation_method" value="ALL"/>
+      <param name="max_fragment_charge" value="3"/>
+      <param name="clip_nterm_methionine" value="false"/>
+      <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
+      <param name="variable_modifications" value="Met-loss (Protein N-term M)"/>
+      <param name="binary_modifications" value=""/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </xml>
   <xml name="autotest_CompNovoCID">
     <test expect_num_outputs="2">
@@ -1006,11 +1069,13 @@
       <output name="out" file="ConsensusID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="false"/>
       <param name="algorithm" value="PEPMatrix"/>
       <section name="filter">
         <param name="considered_hits" value="0"/>
         <param name="min_support" value="0.0"/>
         <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="false"/>
       </section>
       <section name="PEPIons">
         <param name="mass_tolerance" value="0.5"/>
@@ -1037,11 +1102,13 @@
       <output name="out" file="ConsensusID_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="false"/>
       <param name="algorithm" value="average"/>
       <section name="filter">
         <param name="considered_hits" value="0"/>
         <param name="min_support" value="0.0"/>
         <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="false"/>
       </section>
       <section name="PEPIons">
         <param name="mass_tolerance" value="0.5"/>
@@ -1068,11 +1135,13 @@
       <output name="out" file="ConsensusID_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="false"/>
       <param name="algorithm" value="best"/>
       <section name="filter">
         <param name="considered_hits" value="0"/>
         <param name="min_support" value="0.0"/>
         <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="false"/>
       </section>
       <section name="PEPIons">
         <param name="mass_tolerance" value="0.5"/>
@@ -1099,11 +1168,13 @@
       <output name="out" file="ConsensusID_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="false"/>
       <param name="algorithm" value="PEPMatrix"/>
       <section name="filter">
         <param name="considered_hits" value="6"/>
         <param name="min_support" value="0.0"/>
         <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="false"/>
       </section>
       <section name="PEPIons">
         <param name="mass_tolerance" value="0.5"/>
@@ -1130,11 +1201,13 @@
       <output name="out" file="ConsensusID_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="false"/>
       <param name="algorithm" value="PEPIons"/>
       <section name="filter">
         <param name="considered_hits" value="0"/>
         <param name="min_support" value="0.0"/>
         <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="false"/>
       </section>
       <section name="PEPIons">
         <param name="mass_tolerance" value="0.5"/>
@@ -1161,11 +1234,79 @@
       <output name="out" file="ConsensusID_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="false"/>
       <param name="algorithm" value="best"/>
       <section name="filter">
         <param name="considered_hits" value="0"/>
         <param name="min_support" value="0.5"/>
         <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="false"/>
+      </section>
+      <section name="PEPIons">
+        <param name="mass_tolerance" value="0.5"/>
+        <param name="min_shared" value="2"/>
+      </section>
+      <section name="PEPMatrix">
+        <param name="matrix" value="identity"/>
+        <param name="penalty" value="5"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="ConsensusID_6_input.idXML"/>
+      <output name="out" file="ConsensusID_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="rt_delta" value="0.1"/>
+      <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="true"/>
+      <param name="algorithm" value="best"/>
+      <section name="filter">
+        <param name="considered_hits" value="0"/>
+        <param name="min_support" value="0.0"/>
+        <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="true"/>
+      </section>
+      <section name="PEPIons">
+        <param name="mass_tolerance" value="0.5"/>
+        <param name="min_shared" value="2"/>
+      </section>
+      <section name="PEPMatrix">
+        <param name="matrix" value="identity"/>
+        <param name="penalty" value="5"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="ConsensusID_8_input.idXML"/>
+      <output name="out" file="ConsensusID_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="rt_delta" value="0.1"/>
+      <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="true"/>
+      <param name="algorithm" value="best"/>
+      <section name="filter">
+        <param name="considered_hits" value="0"/>
+        <param name="min_support" value="0.0"/>
+        <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="true"/>
       </section>
       <section name="PEPIons">
         <param name="mass_tolerance" value="0.5"/>
@@ -1230,7 +1371,7 @@
       <param name="enzyme" value="trypsin"/>
       <param name="digestion" value="full-digest"/>
       <param name="allowed_missed_cleavages" value="0"/>
-      <param name="decoy_format" value="shuffle"/>
+      <param name="decoy_format" value="peptide-reverse"/>
       <param name="keep_terminal_aminos" value="NC"/>
       <param name="cterm_modifications" value=""/>
       <param name="nterm_modifications" value=""/>
@@ -1317,6 +1458,74 @@
       </output>
     </test>
   </xml>
+  <xml name="autotest_DatabaseSuitability">
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
+      <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
+      <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
+      <output name="out" file="DatabaseSuitability_out_1.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
+      <section name="algorithm">
+        <param name="no_rerank" value="false"/>
+        <param name="reranking_cutoff_percentile" value="0.01"/>
+        <param name="FDR" value="0.8"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
+      <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
+      <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
+      <output name="out" file="DatabaseSuitability_out_2.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
+      <section name="algorithm">
+        <param name="no_rerank" value="false"/>
+        <param name="reranking_cutoff_percentile" value="0.9"/>
+        <param name="FDR" value="1.0"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
+      <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
+      <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
+      <output name="out" file="DatabaseSuitability_out_3.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
+      <section name="algorithm">
+        <param name="no_rerank" value="true"/>
+        <param name="reranking_cutoff_percentile" value="0.01"/>
+        <param name="FDR" value="0.9"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+  </xml>
   <xml name="autotest_Decharger">
     <test expect_num_outputs="4">
       <conditional name="adv_opts_cond">
@@ -1475,6 +1684,8 @@
   </xml>
   <xml name="autotest_DeMeanderize">
 </xml>
+  <xml name="autotest_DigestorMotif">
+</xml>
   <xml name="autotest_Digestor">
 </xml>
   <xml name="autotest_DTAExtractor">
@@ -1546,12 +1757,14 @@
       </conditional>
       <param name="in" value="FidoAdapter_1_input.idXML"/>
       <output name="out" file="Epifany_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="out_type" value="idxml"/>
       <param name="protein_fdr" value="false"/>
       <param name="greedy_group_resolution" value="none"/>
       <param name="max_psms_extreme_probability" value="1.0"/>
       <section name="algorithm">
         <param name="psm_probability_cutoff" value="0.001"/>
         <param name="top_PSMs" value="1"/>
+        <param name="keep_best_PSM_only" value="true"/>
         <param name="update_PSM_probabilities" value="true"/>
         <param name="user_defined_priors" value="false"/>
         <param name="annotate_group_probabilities" value="true"/>
@@ -1574,6 +1787,107 @@
         <section name="param_optimize">
           <param name="aucweight" value="0.3"/>
           <param name="conservative_fdr" value="true"/>
+          <param name="regularized_fdr" value="true"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="conservative_fdr" value="true"/>
+        <param name="min_psms_extreme_probability" value="0.0"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="Epifany_2_input.consensusXML"/>
+      <output name="out" file="Epifany_2_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
+      <param name="out_type" value="consensusXML"/>
+      <param name="protein_fdr" value="false"/>
+      <param name="greedy_group_resolution" value="none"/>
+      <param name="max_psms_extreme_probability" value="1.0"/>
+      <section name="algorithm">
+        <param name="psm_probability_cutoff" value="0.001"/>
+        <param name="top_PSMs" value="1"/>
+        <param name="keep_best_PSM_only" value="true"/>
+        <param name="update_PSM_probabilities" value="true"/>
+        <param name="user_defined_priors" value="false"/>
+        <param name="annotate_group_probabilities" value="true"/>
+        <param name="use_ids_outside_features" value="false"/>
+        <section name="model_parameters">
+          <param name="prot_prior" value="0.7"/>
+          <param name="pep_emission" value="0.1"/>
+          <param name="pep_spurious_emission" value="0.001"/>
+          <param name="pep_prior" value="0.1"/>
+          <param name="regularize" value="false"/>
+          <param name="extended_model" value="false"/>
+        </section>
+        <section name="loopy_belief_propagation">
+          <param name="scheduling_type" value="priority"/>
+          <param name="convergence_threshold" value="1e-05"/>
+          <param name="dampening_lambda" value="0.001"/>
+          <param name="max_nr_iterations" value="2147483647"/>
+          <param name="p_norm_inference" value="1.0"/>
+        </section>
+        <section name="param_optimize">
+          <param name="aucweight" value="0.3"/>
+          <param name="conservative_fdr" value="true"/>
+          <param name="regularized_fdr" value="true"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="conservative_fdr" value="true"/>
+        <param name="min_psms_extreme_probability" value="0.0"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="Epifany_2_input.consensusXML"/>
+      <output name="out" file="Epifany_3_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
+      <param name="out_type" value="consensusXML"/>
+      <param name="protein_fdr" value="false"/>
+      <param name="greedy_group_resolution" value="none"/>
+      <param name="max_psms_extreme_probability" value="1.0"/>
+      <section name="algorithm">
+        <param name="psm_probability_cutoff" value="0.001"/>
+        <param name="top_PSMs" value="1"/>
+        <param name="keep_best_PSM_only" value="false"/>
+        <param name="update_PSM_probabilities" value="true"/>
+        <param name="user_defined_priors" value="false"/>
+        <param name="annotate_group_probabilities" value="true"/>
+        <param name="use_ids_outside_features" value="false"/>
+        <section name="model_parameters">
+          <param name="prot_prior" value="0.7"/>
+          <param name="pep_emission" value="0.1"/>
+          <param name="pep_spurious_emission" value="0.001"/>
+          <param name="pep_prior" value="0.1"/>
+          <param name="regularize" value="false"/>
+          <param name="extended_model" value="false"/>
+        </section>
+        <section name="loopy_belief_propagation">
+          <param name="scheduling_type" value="priority"/>
+          <param name="convergence_threshold" value="1e-05"/>
+          <param name="dampening_lambda" value="0.001"/>
+          <param name="max_nr_iterations" value="2147483647"/>
+          <param name="p_norm_inference" value="1.0"/>
+        </section>
+        <section name="param_optimize">
+          <param name="aucweight" value="0.3"/>
+          <param name="conservative_fdr" value="true"/>
+          <param name="regularized_fdr" value="true"/>
         </section>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -1976,6 +2290,7 @@
         <param name="add_zeros" value="0.2"/>
         <param name="unweighted_fit" value="false"/>
         <param name="no_imputation" value="false"/>
+        <param name="each_trace" value="false"/>
         <section name="check">
           <param name="min_area" value="1.0"/>
           <param name="boundaries" value="0.5"/>
@@ -2031,61 +2346,7 @@
         <param name="add_zeros" value="0.2"/>
         <param name="unweighted_fit" value="false"/>
         <param name="no_imputation" value="false"/>
-        <section name="check">
-          <param name="min_area" value="1.0"/>
-          <param name="boundaries" value="0.5"/>
-          <param name="width" value="10.0"/>
-          <param name="asymmetry" value="10.0"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
-      <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
-      <output name="out" file="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="extract">
-        <param name="batch_size" value="10"/>
-        <param name="mz_window" value="0.1"/>
-        <param name="n_isotopes" value="2"/>
-        <param name="isotope_pmin" value="0.0"/>
-        <param name="rt_quantile" value="0.95"/>
-        <param name="rt_window" value="0.0"/>
-      </section>
-      <section name="detect">
-        <param name="peak_width" value="60.0"/>
-        <param name="min_peak_width" value="0.2"/>
-        <param name="signal_to_noise" value="0.8"/>
-        <param name="mapping_tolerance" value="0.0"/>
-      </section>
-      <section name="svm">
-        <param name="samples" value="0"/>
-        <param name="no_selection" value="false"/>
-        <param name="kernel" value="RBF"/>
-        <param name="xval" value="5"/>
-        <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/>
-        <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/>
-        <param name="epsilon" value="0.001"/>
-        <param name="cache_size" value="100.0"/>
-        <param name="no_shrinking" value="false"/>
-        <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/>
-        <param name="min_prob" value="0.0"/>
-      </section>
-      <section name="model">
-        <param name="type" value="none"/>
-        <param name="add_zeros" value="0.2"/>
-        <param name="unweighted_fit" value="false"/>
-        <param name="no_imputation" value="false"/>
+        <param name="each_trace" value="false"/>
         <section name="check">
           <param name="min_area" value="1.0"/>
           <param name="boundaries" value="0.5"/>
@@ -2129,6 +2390,7 @@
         <param name="add_zeros" value="0.2"/>
         <param name="unweighted_fit" value="false"/>
         <param name="no_imputation" value="false"/>
+        <param name="each_trace" value="false"/>
         <section name="check">
           <param name="min_area" value="1.0"/>
           <param name="boundaries" value="0.5"/>
@@ -4074,7 +4336,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="FidoAdapter_1_input.idXML"/>
-      <output name="out" file="FidoAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <output name="out" file="FidoAdapter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
       <param name="separate_runs" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="no_cleanup" value="false"/>
@@ -5009,6 +5271,34 @@
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
+      <param name="in" value="FileConverter_32_input.mzML"/>
+      <output name="out" file="FileConverter_32_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
+      <param name="out_type" value="mzML"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="UID_postprocessing" value="ensure"/>
+        <param name="TIC_DTA2D" value="false"/>
+        <param name="MGF_compact" value="false"/>
+        <param name="force_MaxQuant_compatibility" value="false"/>
+        <param name="convert_to_chromatograms" value="false"/>
+        <param name="force_TPP_compatibility" value="false"/>
+        <param name="change_im_format" value="none"/>
+        <param name="write_scan_index" value="true"/>
+        <param name="lossy_compression" value="false"/>
+        <param name="lossy_mass_accuracy" value="-1.0"/>
+        <param name="process_lowmemory" value="false"/>
+        <param name="no_peak_picking" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
       <param name="in" value="ginkgotoxin-ms-switching.raw"/>
       <output name="out" file="ginkgotoxin-ms-switching_out_tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
       <param name="out_type" value="mzml"/>
@@ -11129,6 +11419,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11154,6 +11446,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11179,6 +11473,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11203,6 +11499,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11228,6 +11526,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11253,6 +11553,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11277,6 +11579,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11301,6 +11605,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11325,6 +11631,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11349,6 +11657,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11373,6 +11683,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11397,6 +11709,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11421,6 +11735,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11445,6 +11761,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11470,6 +11788,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11494,6 +11814,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11518,6 +11840,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11542,6 +11866,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11566,6 +11892,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11590,6 +11918,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11615,6 +11945,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.01"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11640,6 +11972,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11664,6 +11998,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11688,6 +12024,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11712,6 +12050,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11728,6 +12068,136 @@
         </assert_contents>
       </output>
     </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="ignore_proteins_per_peptide" value="false"/>
+        <param name="scan_regex" value=""/>
+        <param name="no_spectra_data_override" value="false"/>
+        <param name="no_spectra_references_override" value="false"/>
+        <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="IDFileConverter_27_input.idXML"/>
+      <output name="out" file="IDFileConverter_27_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
+      <param name="out_type" value="FASTA"/>
+      <param name="mz_name" value=""/>
+      <param name="peptideprophet_analyzed" value="false"/>
+      <param name="score_type" value="qvalue"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="ignore_proteins_per_peptide" value="false"/>
+        <param name="scan_regex" value=""/>
+        <param name="no_spectra_data_override" value="false"/>
+        <param name="no_spectra_references_override" value="false"/>
+        <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="-1"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="IDFileConverter_27_input.idXML"/>
+      <output name="out" file="IDFileConverter_28_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
+      <param name="out_type" value="FASTA"/>
+      <param name="mz_name" value=""/>
+      <param name="peptideprophet_analyzed" value="false"/>
+      <param name="score_type" value="qvalue"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="ignore_proteins_per_peptide" value="false"/>
+        <param name="scan_regex" value=""/>
+        <param name="no_spectra_data_override" value="false"/>
+        <param name="no_spectra_references_override" value="false"/>
+        <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="true"/>
+        <param name="number_of_hits" value="1"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="IDFileConverter_27_input.idXML"/>
+      <output name="out" file="IDFileConverter_29_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
+      <param name="out_type" value="FASTA"/>
+      <param name="mz_name" value=""/>
+      <param name="peptideprophet_analyzed" value="false"/>
+      <param name="score_type" value="qvalue"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="ignore_proteins_per_peptide" value="false"/>
+        <param name="scan_regex" value=""/>
+        <param name="no_spectra_data_override" value="false"/>
+        <param name="no_spectra_references_override" value="false"/>
+        <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="true"/>
+        <param name="number_of_hits" value="2"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="IDFileConverter_27_input.idXML"/>
+      <output name="out" file="IDFileConverter_30_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
+      <param name="out_type" value="FASTA"/>
+      <param name="mz_name" value=""/>
+      <param name="peptideprophet_analyzed" value="false"/>
+      <param name="score_type" value="qvalue"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="ignore_proteins_per_peptide" value="false"/>
+        <param name="scan_regex" value=""/>
+        <param name="no_spectra_data_override" value="false"/>
+        <param name="no_spectra_references_override" value="false"/>
+        <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="IDFileConverter_31_input.mzid"/>
+      <output name="out" file="IDFileConverter_31_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="out_type" value="idXML"/>
+      <param name="mz_name" value=""/>
+      <param name="peptideprophet_analyzed" value="false"/>
+      <param name="score_type" value="qvalue"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </xml>
   <xml name="autotest_IDFilter">
     <test expect_num_outputs="2">
@@ -11754,6 +12224,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="proteins" value="IDFilter_1_input.fas"/>
@@ -11821,6 +12292,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -11888,6 +12360,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -11954,6 +12427,7 @@
       <section name="score">
         <param name="pep" value="32.0"/>
         <param name="prot" value="25.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12020,6 +12494,7 @@
       <section name="score">
         <param name="pep" value="32.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12086,6 +12561,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="25.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12152,6 +12628,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="25.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12218,6 +12695,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12284,6 +12762,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12350,6 +12829,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12416,6 +12896,7 @@
       <section name="score">
         <param name="pep" value="0.05"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12482,6 +12963,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.3"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12548,6 +13030,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12614,6 +13097,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12681,6 +13165,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12748,6 +13233,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12815,6 +13301,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12882,6 +13369,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12949,6 +13437,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -13015,6 +13504,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -13081,6 +13571,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -13147,6 +13638,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -13213,6 +13705,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -13279,6 +13772,141 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
+      </section>
+      <section name="whitelist">
+        <param name="protein_accessions" value=""/>
+        <param name="ignore_modifications" value="false"/>
+        <param name="modifications" value=""/>
+      </section>
+      <section name="blacklist">
+        <param name="protein_accessions" value=""/>
+        <param name="ignore_modifications" value="false"/>
+        <param name="modifications" value=""/>
+      </section>
+      <section name="in_silico_digestion">
+        <param name="enzyme" value="Trypsin"/>
+        <param name="specificity" value="full"/>
+        <param name="missed_cleavages" value="-1"/>
+        <param name="methionine_cleavage" value="false"/>
+      </section>
+      <section name="missed_cleavages">
+        <param name="number_of_missed_cleavages" value=":"/>
+        <param name="enzyme" value="Trypsin"/>
+      </section>
+      <section name="rt">
+        <param name="p_value" value="0.0"/>
+        <param name="p_value_1st_dim" value="0.0"/>
+      </section>
+      <section name="mz">
+        <param name="error" value="-1.0"/>
+        <param name="unit" value="ppm"/>
+      </section>
+      <section name="best">
+        <param name="n_peptide_hits" value="0"/>
+        <param name="n_protein_hits" value="0"/>
+        <param name="strict" value="false"/>
+        <param name="n_to_m_peptide_hits" value=":"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="remove_duplicate_psm" value="false"/>
+        <param name="remove_peptide_hits_by_metavalue" value=""/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="IDMapper_2_output.consensusXML"/>
+      <output name="out" file="IDFilter_23_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
+      <param name="var_mods" value="false"/>
+      <param name="remove_shared_peptides" value="false"/>
+      <param name="keep_unreferenced_protein_hits" value="false"/>
+      <param name="remove_decoys" value="false"/>
+      <param name="delete_unreferenced_peptide_hits" value="false"/>
+      <section name="precursor">
+        <param name="rt" value=":"/>
+        <param name="mz" value=":"/>
+        <param name="length" value=":"/>
+        <param name="charge" value=":"/>
+      </section>
+      <section name="score">
+        <param name="pep" value="0.0"/>
+        <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
+      </section>
+      <section name="whitelist">
+        <param name="protein_accessions" value="&quot;Q9HP81&quot;"/>
+        <param name="ignore_modifications" value="false"/>
+        <param name="modifications" value=""/>
+      </section>
+      <section name="blacklist">
+        <param name="protein_accessions" value=""/>
+        <param name="ignore_modifications" value="false"/>
+        <param name="modifications" value=""/>
+      </section>
+      <section name="in_silico_digestion">
+        <param name="enzyme" value="Trypsin"/>
+        <param name="specificity" value="full"/>
+        <param name="missed_cleavages" value="-1"/>
+        <param name="methionine_cleavage" value="false"/>
+      </section>
+      <section name="missed_cleavages">
+        <param name="number_of_missed_cleavages" value=":"/>
+        <param name="enzyme" value="Trypsin"/>
+      </section>
+      <section name="rt">
+        <param name="p_value" value="0.0"/>
+        <param name="p_value_1st_dim" value="0.0"/>
+      </section>
+      <section name="mz">
+        <param name="error" value="-1.0"/>
+        <param name="unit" value="ppm"/>
+      </section>
+      <section name="best">
+        <param name="n_peptide_hits" value="0"/>
+        <param name="n_protein_hits" value="0"/>
+        <param name="strict" value="false"/>
+        <param name="n_to_m_peptide_hits" value=":"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="remove_duplicate_psm" value="false"/>
+        <param name="remove_peptide_hits_by_metavalue" value=""/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="Epifany_3_out.consensusXML"/>
+      <output name="out" file="IDFilter_24_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
+      <param name="var_mods" value="false"/>
+      <param name="remove_shared_peptides" value="false"/>
+      <param name="keep_unreferenced_protein_hits" value="false"/>
+      <param name="remove_decoys" value="false"/>
+      <param name="delete_unreferenced_peptide_hits" value="false"/>
+      <section name="precursor">
+        <param name="rt" value=":"/>
+        <param name="mz" value=":"/>
+        <param name="length" value=":"/>
+        <param name="charge" value=":"/>
+      </section>
+      <section name="score">
+        <param name="pep" value="0.0"/>
+        <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.99"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -13882,11 +14510,11 @@
       </conditional>
       <param name="in" value="IDFileConverter_12_output.idXML"/>
       <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="proteins" value="false"/>
       <param name="new_score" value="Percolator_PEP"/>
       <param name="new_score_orientation" value="lower_better"/>
       <param name="new_score_type" value="Posterior Error Probability"/>
       <param name="old_score" value="Percolator_qvalue"/>
-      <param name="proteins" value="false"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
@@ -13902,11 +14530,11 @@
       </conditional>
       <param name="in" value="IDScoreSwitcher_2_input.idXML"/>
       <output name="out" file="IDScoreSwitcher_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="proteins" value="true"/>
       <param name="new_score" value="Posterior Probability_score"/>
       <param name="new_score_orientation" value="higher_better"/>
       <param name="new_score_type" value="Posterior Probability"/>
       <param name="old_score" value=""/>
-      <param name="proteins" value="true"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
@@ -14453,80 +15081,6 @@
   </xml>
   <xml name="autotest_LabeledEval">
 </xml>
-  <xml name="autotest_LowMemPeakPickerHiResRandomAccess">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerHiRes_RandomAccess_input.mzML"/>
-      <output name="out" file="LowMemPeakPickerHiRes_RandomAccess_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="1.0"/>
-        <param name="spacing_difference_gap" value="4.0"/>
-        <param name="spacing_difference" value="1.5"/>
-        <param name="missing" value="1"/>
-        <param name="ms_levels" value="1"/>
-        <param name="report_FWHM" value="false"/>
-        <param name="report_FWHM_unit" value="relative"/>
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_LowMemPeakPickerHiRes">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerHiRes_input.mzML"/>
-      <output name="out" file="LowMemPeakPickerHiRes_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="1.0"/>
-        <param name="spacing_difference_gap" value="4.0"/>
-        <param name="spacing_difference" value="1.5"/>
-        <param name="missing" value="1"/>
-        <param name="ms_levels" value="1"/>
-        <param name="report_FWHM" value="false"/>
-        <param name="report_FWHM_unit" value="relative"/>
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
   <xml name="autotest_LuciphorAdapter">
     <test expect_num_outputs="2">
       <conditional name="adv_opts_cond">
@@ -14894,6 +15448,63 @@
         </assert_contents>
       </output>
     </test>
+    <test expect_num_outputs="3">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="true"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="MapAlignerIdentification_7_input1.idXML"/>
+      <output_collection name="out" count="1"/>
+      <output_collection name="trafo_out" count="1"/>
+      <section name="reference">
+        <param name="file" value="MapAlignerIdentification_7_input2.idXML"/>
+        <param name="index" value="0"/>
+      </section>
+      <section name="algorithm">
+        <param name="score_cutoff" value="false"/>
+        <param name="min_score" value="0.05"/>
+        <param name="min_run_occur" value="2"/>
+        <param name="max_rt_shift" value="0.5"/>
+        <param name="use_unassigned_peptides" value="true"/>
+        <param name="use_feature_rt" value="false"/>
+      </section>
+      <section name="model">
+        <param name="type" value="b_spline"/>
+        <section name="linear">
+          <param name="symmetric_regression" value="false"/>
+          <param name="x_weight" value=""/>
+          <param name="y_weight" value=""/>
+          <param name="x_datum_min" value="1e-15"/>
+          <param name="x_datum_max" value="1000000000000000.0"/>
+          <param name="y_datum_min" value="1e-15"/>
+          <param name="y_datum_max" value="1000000000000000.0"/>
+        </section>
+        <section name="b_spline">
+          <param name="wavelength" value="0.0"/>
+          <param name="num_nodes" value="5"/>
+          <param name="extrapolate" value="linear"/>
+          <param name="boundary_condition" value="2"/>
+        </section>
+        <section name="lowess">
+          <param name="span" value="0.666666666666667"/>
+          <param name="num_iterations" value="3"/>
+          <param name="delta" value="-1.0"/>
+          <param name="interpolation_type" value="cspline"/>
+          <param name="extrapolation_type" value="four-point-linear"/>
+        </section>
+        <section name="interpolated">
+          <param name="interpolation_type" value="cspline"/>
+          <param name="extrapolation_type" value="two-point-linear"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </xml>
   <xml name="autotest_MapAlignerPoseClustering">
     <test expect_num_outputs="3">
@@ -15281,6 +15892,61 @@
         </assert_contents>
       </output>
     </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/>
+      <output_collection name="out" count="3"/>
+      <section name="algorithm">
+        <param name="model_type" value="b_spline"/>
+        <section name="model">
+          <param name="type" value="b_spline"/>
+          <section name="linear">
+            <param name="symmetric_regression" value="false"/>
+            <param name="x_weight" value=""/>
+            <param name="y_weight" value=""/>
+            <param name="x_datum_min" value="1e-15"/>
+            <param name="x_datum_max" value="1000000000000000.0"/>
+            <param name="y_datum_min" value="1e-15"/>
+            <param name="y_datum_max" value="1000000000000000.0"/>
+          </section>
+          <section name="b_spline">
+            <param name="wavelength" value="0.0"/>
+            <param name="num_nodes" value="5"/>
+            <param name="extrapolate" value="linear"/>
+            <param name="boundary_condition" value="2"/>
+          </section>
+          <section name="lowess">
+            <param name="span" value="0.666666666666667"/>
+            <param name="num_iterations" value="3"/>
+            <param name="delta" value="-1.0"/>
+            <param name="interpolation_type" value="cspline"/>
+            <param name="extrapolation_type" value="four-point-linear"/>
+          </section>
+          <section name="interpolated">
+            <param name="interpolation_type" value="cspline"/>
+            <param name="extrapolation_type" value="two-point-linear"/>
+          </section>
+        </section>
+        <section name="align_algorithm">
+          <param name="score_cutoff" value="false"/>
+          <param name="min_score" value="0.05"/>
+          <param name="min_run_occur" value="2"/>
+          <param name="max_rt_shift" value="0.5"/>
+          <param name="use_unassigned_peptides" value="true"/>
+          <param name="use_feature_rt" value="true"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </xml>
   <xml name="autotest_MapNormalizer">
     <test expect_num_outputs="2">
@@ -15651,9 +16317,8 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="MascotAdapter_1_input.mzData"/>
-      <output name="out" file="output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="mascot_in" value="true"/>
-      <param name="mascot_out" value="false"/>
+      <output name="out" file="MascotAdapter_1_output.mascot_in" compare="sim_size" delta="5700"/>
+      <param name="out_type" value="mgf"/>
       <param name="instrument" value="ESI-TRAP"/>
       <param name="precursor_mass_tolerance" value="1.3"/>
       <param name="peak_mass_tolerance" value="0.3"/>
@@ -15691,8 +16356,7 @@
       </conditional>
       <param name="in" value="MascotAdapter_2_input.mascotXML"/>
       <output name="out" file="MascotAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="mascot_in" value="false"/>
-      <param name="mascot_out" value="true"/>
+      <param name="out_type" value="idXML"/>
       <param name="instrument" value="Default"/>
       <param name="precursor_mass_tolerance" value="2.0"/>
       <param name="peak_mass_tolerance" value="1.0"/>
@@ -15730,9 +16394,9 @@
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
-      <param name="in" value="MassCalculator_1_input.txt" ftype="txt"/>
+      <param name="in" value="MassCalculator_1_input.tsv" ftype="tabular"/>
       <param name="in_seq" value=""/>
-      <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta="5700" ftype="txt"/>
+      <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta="5700" ftype="csv"/>
       <param name="charge" value="0 1"/>
       <param name="format" value="table"/>
       <param name="average_mass" value="false"/>
@@ -15752,7 +16416,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in_seq" value="&quot;LDQWLC(Carbamidomethyl)EKL&quot; &quot;(Glu-&gt;pyro-Glu)EAM(Oxidation)APKHK&quot; &quot;RANVM(Oxidation)DYR&quot; &quot;FGVEQDVDMVFASFIR&quot;"/>
-      <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
+      <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
       <param name="charge" value="1 2 3"/>
       <param name="format" value="list"/>
       <param name="average_mass" value="false"/>
@@ -15849,7 +16513,80 @@
     </test>
   </xml>
   <xml name="autotest_MetaboliteAdductDecharger">
-</xml>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/>
+      <output name="out_fm" file="MetaboliteAdductDecharger_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
+      <section name="algorithm">
+        <section name="MetaboliteFeatureDeconvolution">
+          <param name="charge_min" value="1"/>
+          <param name="charge_max" value="3"/>
+          <param name="charge_span_max" value="3"/>
+          <param name="q_try" value="feature"/>
+          <param name="retention_max_diff" value="1.0"/>
+          <param name="retention_max_diff_local" value="1.0"/>
+          <param name="mass_max_diff" value="0.05"/>
+          <param name="unit" value="Da"/>
+          <param name="potential_adducts" value="&quot;H:+:0.4&quot; &quot;Na:+:0.25&quot; &quot;NH4:+:0.25&quot; &quot;K:+:0.1&quot; &quot;H-2O-1:0:0.05&quot;"/>
+          <param name="max_neutrals" value="1"/>
+          <param name="use_minority_bound" value="true"/>
+          <param name="max_minority_bound" value="3"/>
+          <param name="min_rt_overlap" value="0.66"/>
+          <param name="intensity_filter" value="false"/>
+          <param name="negative_mode" value="false"/>
+          <param name="default_map_label" value="decharged features"/>
+          <param name="verbose_level" value="0"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="3">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/>
+      <output name="out_cm" file="MetaboliteAdductDecharger_2_output_1.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
+      <output name="outpairs" file="MetaboliteAdductDecharger_2_output_2.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
+      <section name="algorithm">
+        <section name="MetaboliteFeatureDeconvolution">
+          <param name="charge_min" value="1"/>
+          <param name="charge_max" value="3"/>
+          <param name="charge_span_max" value="3"/>
+          <param name="q_try" value="feature"/>
+          <param name="retention_max_diff" value="1.0"/>
+          <param name="retention_max_diff_local" value="1.0"/>
+          <param name="mass_max_diff" value="0.05"/>
+          <param name="unit" value="Da"/>
+          <param name="potential_adducts" value="&quot;H:+:0.4&quot; &quot;Na:+:0.25&quot; &quot;NH4:+:0.25&quot; &quot;K:+:0.1&quot; &quot;H-2O-1:0:0.05&quot;"/>
+          <param name="max_neutrals" value="1"/>
+          <param name="use_minority_bound" value="true"/>
+          <param name="max_minority_bound" value="3"/>
+          <param name="min_rt_overlap" value="0.66"/>
+          <param name="intensity_filter" value="false"/>
+          <param name="negative_mode" value="false"/>
+          <param name="default_map_label" value="decharged features"/>
+          <param name="verbose_level" value="0"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_cm_FLAG,outpairs_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+  </xml>
   <xml name="autotest_MetaboliteSpectralMatcher">
 </xml>
   <xml name="autotest_MetaProSIP">
@@ -16055,6 +16792,7 @@
     <test expect_num_outputs="3">
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
+        <param name="add_decoys" value="false"/>
         <param name="legacy_conversion" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -16063,7 +16801,6 @@
       <output name="out" file="MSGFPlusAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
       <output name="mzid_out" file="MSGFPlusAdapter_1_out2.tmp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
       <param name="database" value="proteins.fasta"/>
-      <param name="add_decoys" value="false"/>
       <param name="precursor_mass_tolerance" value="10.0"/>
       <param name="precursor_error_units" value="ppm"/>
       <param name="isotope_error_range" value="0,1"/>
@@ -16079,6 +16816,8 @@
       <param name="matches_per_spec" value="1"/>
       <param name="add_features" value="false"/>
       <param name="max_mods" value="2"/>
+      <param name="max_missed_cleavages" value="-1"/>
+      <param name="tasks" value="0"/>
       <param name="fixed_modifications" value=""/>
       <param name="variable_modifications" value="Oxidation (M)"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mzid_out_FLAG"/>
@@ -16413,6 +17152,74 @@
         </assert_contents>
       </output>
     </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="first_run_inference_only" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="Epifany_2_out.consensusXML"/>
+      <output name="out" file="MzTabExporter_4_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
+      <param name="opt_columns" value="subfeatures"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="first_run_inference_only" value="true"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="MzTabExporter_5_in.consensusXML"/>
+      <output name="out" file="MzTabExporter_5_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
+      <param name="opt_columns" value="subfeatures"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="first_run_inference_only" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="MzTabExporter_6_input.idXML"/>
+      <output name="out" file="MzTabExporter_6_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
+      <param name="opt_columns" value="subfeatures"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="first_run_inference_only" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="MzTabExporter_7_input.consensusXML"/>
+      <output name="out" file="MzTabExporter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
+      <param name="opt_columns" value="subfeatures"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </xml>
   <xml name="autotest_NoiseFilterGaussian">
     <test expect_num_outputs="2">
@@ -16919,6 +17726,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17030,6 +17838,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17141,6 +17950,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17252,6 +18062,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17362,6 +18173,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17473,6 +18285,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17584,6 +18397,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17695,6 +18509,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17806,6 +18621,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -18290,6 +19106,8 @@
       </output>
     </test>
   </xml>
+  <xml name="autotest_OpenSwathDIAPreScoring">
+</xml>
   <xml name="autotest_OpenSwathFeatureXMLToTSV">
     <test expect_num_outputs="2">
       <conditional name="adv_opts_cond">
@@ -18594,6 +19412,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -18715,6 +19534,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -18836,6 +19656,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -18932,17 +19753,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="false"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="false"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -18951,10 +19772,10 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
@@ -18965,8 +19786,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -18994,7 +19815,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -19008,10 +19829,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -19023,7 +19845,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -19067,13 +19889,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -19089,17 +19911,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_2_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="false"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="false"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -19108,10 +19930,10 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_2_input.mzXML"/>
       <param name="tr" value="OpenSwathWorkflow_2_input.TraML"/>
@@ -19121,8 +19943,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -19150,7 +19972,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -19164,10 +19986,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -19179,7 +20002,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -19223,13 +20046,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -19245,17 +20068,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -19264,10 +20087,10 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
@@ -19277,8 +20100,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -19306,7 +20129,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -19320,10 +20143,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -19335,7 +20159,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -19379,13 +20203,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -19401,17 +20225,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -19420,10 +20244,10 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
@@ -19433,8 +20257,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -19462,7 +20286,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -19476,10 +20300,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -19491,7 +20316,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -19535,13 +20360,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -19557,17 +20382,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -19576,10 +20401,10 @@
         <param name="readOptions" value="cache"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
@@ -19589,8 +20414,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -19618,7 +20443,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -19632,10 +20457,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -19647,7 +20473,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -19691,13 +20517,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -19713,17 +20539,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -19732,10 +20558,10 @@
         <param name="readOptions" value="cacheWorkingInMemory"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
@@ -19745,8 +20571,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -19774,7 +20600,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -19788,10 +20614,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -19803,7 +20630,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -19847,13 +20674,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -19868,19 +20695,18 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="swath_windows_file" value="swath_windows.txt" ftype="txt"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -19889,21 +20715,22 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
       <param name="tr_type" value=""/>
+      <param name="swath_windows_file" value="swath_windows.txt" ftype="txt"/>
       <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
       <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -19931,7 +20758,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -19945,10 +20772,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -19960,7 +20788,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -20004,13 +20832,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -20025,19 +20853,18 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="swath_windows_file" value="swath_windows_overlap.txt" ftype="txt"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -20046,21 +20873,22 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
         <param name="force" value="true"/>
-        <param name="test" value="true"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
       <param name="tr_type" value=""/>
+      <param name="swath_windows_file" value="swath_windows_overlap.txt" ftype="txt"/>
       <output name="out_features" file="OpenSwathWorkflow_10.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
       <output name="out_chrom" file="OpenSwathWorkflow_10.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -20088,7 +20916,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -20102,10 +20930,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -20117,7 +20946,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -20161,13 +20990,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -20182,13 +21011,13 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="false"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="false"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
         <param name="irt_mz_extraction_window" value="550.0"/>
@@ -20201,10 +21030,10 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="quadratic_regression_delta_ppm"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_11_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_11_input_2.TraML"/>
@@ -20216,7 +21045,7 @@
       <param name="rt_extraction_window" value="-1.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
       <param name="mz_extraction_window" value="0.2"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -20244,7 +21073,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -20258,10 +21087,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -20273,7 +21103,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -20317,13 +21147,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="true"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -20339,17 +21169,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -20358,10 +21188,10 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_13_input.pqp.tmp"/>
@@ -20371,8 +21201,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -20400,7 +21230,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -20414,10 +21244,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -20429,7 +21260,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -20473,13 +21304,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -20495,17 +21326,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="sqMass"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -20514,10 +21345,10 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_14_input.pqp.tmp"/>
@@ -20527,8 +21358,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -20556,7 +21387,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -20570,10 +21401,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -20585,7 +21417,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -20629,13 +21461,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -20651,17 +21483,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
         <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -20670,7 +21502,7 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
+        <param name="batchSize" value="1000"/>
         <param name="ms1_isotopes" value="2"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -20684,7 +21516,7 @@
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
       <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -20712,7 +21544,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -20726,10 +21558,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -20807,17 +21640,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -20826,10 +21659,10 @@
         <param name="readOptions" value="workingInMemory"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
+        <param name="batchSize" value="1000"/>
         <param name="ms1_isotopes" value="2"/>
         <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_16_input.sqMass"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
@@ -20839,8 +21672,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -20868,7 +21701,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -20882,10 +21715,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -20897,7 +21731,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -20941,13 +21775,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -20962,17 +21796,17 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="false"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -20981,10 +21815,10 @@
         <param name="readOptions" value="workingInMemory"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
@@ -20994,8 +21828,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="0.05"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -21023,7 +21857,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -21037,10 +21871,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -21052,7 +21887,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -21096,13 +21931,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="true"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -21117,17 +21952,17 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="false"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -21136,10 +21971,10 @@
         <param name="readOptions" value="cache"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
@@ -21149,8 +21984,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="0.05"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -21178,7 +22013,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -21192,10 +22027,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -21207,7 +22043,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -21251,13 +22087,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="true"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -21272,17 +22108,17 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="false"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -21291,10 +22127,10 @@
         <param name="readOptions" value="workingInMemory"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_17_input.pqp.tmp"/>
@@ -21304,8 +22140,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="0.05"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -21333,7 +22169,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -21347,10 +22183,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -21362,7 +22199,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -21406,13 +22243,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -21428,16 +22265,16 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
         <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -21446,7 +22283,7 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
+        <param name="batchSize" value="1000"/>
         <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -21459,7 +22296,7 @@
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
       <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -21487,7 +22324,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -21501,10 +22338,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -21582,16 +22420,16 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
         <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -21600,7 +22438,7 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
+        <param name="batchSize" value="1000"/>
         <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -21613,7 +22451,7 @@
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
       <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -21641,7 +22479,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -21655,10 +22493,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -21736,16 +22575,16 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
         <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -21754,7 +22593,7 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
+        <param name="batchSize" value="1000"/>
         <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -21767,7 +22606,7 @@
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
       <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -21795,7 +22634,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -21809,10 +22648,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -21889,17 +22729,17 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
         <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -21908,7 +22748,7 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
+        <param name="batchSize" value="1000"/>
         <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -21923,7 +22763,7 @@
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
       <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <output name="Debugging_irt_trafo" file="OpenSwathWorkflow_21_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
@@ -21952,7 +22792,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.6666666666666666"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -21966,10 +22806,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -22046,17 +22887,17 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="true"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -22065,10 +22906,10 @@
         <param name="readOptions" value="workingInMemory"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
+        <param name="batchSize" value="1000"/>
         <param name="ms1_isotopes" value="3"/>
         <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_22_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_22_input.tsv" ftype="tabular"/>
@@ -22078,8 +22919,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -22107,7 +22948,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -22121,10 +22962,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -22136,7 +22978,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -22180,13 +23022,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -22207,7 +23049,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="PeakPickerHiRes_input.mzML"/>
-      <output name="out" file="PeakPickerHiRes_1.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
+      <output name="out" file="PeakPickerHiRes_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
       <section name="algorithm">
         <param name="signal_to_noise" value="1.0"/>
         <param name="spacing_difference_gap" value="4.0"/>
@@ -22762,12 +23604,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -22792,12 +23634,12 @@
       <param name="write_protein_sequence" value="true"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -22822,12 +23664,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="true"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -22852,12 +23694,12 @@
       <param name="write_protein_sequence" value="true"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="0"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -22882,12 +23724,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -22912,12 +23754,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="3"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -22942,12 +23784,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="full"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -22972,12 +23814,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="semi"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -23002,12 +23844,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="remove"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -23032,13 +23874,13 @@
       <param name="write_protein_sequence" value="true"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="false"/>
+      <param name="unmatched_action" value="error"/>
       <param name="aaa_max" value="3"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="true"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
-        <param name="specificity" value="full"/>
+        <param name="name" value="auto"/>
+        <param name="specificity" value="auto"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -23062,12 +23904,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -23092,13 +23934,13 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="false"/>
+      <param name="unmatched_action" value="error"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
-        <param name="specificity" value="full"/>
+        <param name="name" value="auto"/>
+        <param name="specificity" value="auto"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -23122,12 +23964,12 @@
       <param name="write_protein_sequence" value="true"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="false"/>
+      <param name="unmatched_action" value="error"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -23149,7 +23991,9 @@
         <param name="testFDR" value="0.5"/>
         <param name="trainFDR" value="0.5"/>
         <param name="maxiter" value="10"/>
+        <param name="nested_xval_bins" value="1"/>
         <param name="quick_validation" value="false"/>
+        <param name="static" value="false"/>
         <param name="default_direction" value=""/>
         <param name="verbose" value="2"/>
         <param name="unitnorm" value="false"/>
@@ -23192,7 +24036,9 @@
         <param name="testFDR" value="0.01"/>
         <param name="trainFDR" value="0.01"/>
         <param name="maxiter" value="10"/>
+        <param name="nested_xval_bins" value="1"/>
         <param name="quick_validation" value="false"/>
+        <param name="static" value="false"/>
         <param name="default_direction" value=""/>
         <param name="verbose" value="2"/>
         <param name="unitnorm" value="false"/>
@@ -23235,7 +24081,9 @@
         <param name="testFDR" value="0.01"/>
         <param name="trainFDR" value="0.01"/>
         <param name="maxiter" value="10"/>
+        <param name="nested_xval_bins" value="1"/>
         <param name="quick_validation" value="false"/>
+        <param name="static" value="false"/>
         <param name="default_direction" value=""/>
         <param name="verbose" value="2"/>
         <param name="unitnorm" value="false"/>
@@ -23278,7 +24126,9 @@
         <param name="testFDR" value="0.01"/>
         <param name="trainFDR" value="0.01"/>
         <param name="maxiter" value="10"/>
+        <param name="nested_xval_bins" value="1"/>
         <param name="quick_validation" value="false"/>
+        <param name="static" value="false"/>
         <param name="default_direction" value=""/>
         <param name="verbose" value="2"/>
         <param name="unitnorm" value="false"/>
@@ -23321,7 +24171,9 @@
         <param name="testFDR" value="0.5"/>
         <param name="trainFDR" value="0.5"/>
         <param name="maxiter" value="10"/>
+        <param name="nested_xval_bins" value="1"/>
         <param name="quick_validation" value="false"/>
+        <param name="static" value="false"/>
         <param name="default_direction" value=""/>
         <param name="verbose" value="2"/>
         <param name="unitnorm" value="false"/>
@@ -23539,6 +24391,7 @@
       <param name="annotate_indist_groups" value="true"/>
       <section name="Merging">
         <param name="annotate_origin" value="false"/>
+        <param name="allow_disagreeing_settings" value="false"/>
       </section>
       <section name="Algorithm">
         <param name="min_peptides_per_protein" value="1"/>
@@ -23808,7 +24661,7 @@
         </assert_contents>
       </output>
     </test>
-    <test expect_num_outputs="2">
+    <test expect_num_outputs="3">
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="force" value="false"/>
@@ -23816,6 +24669,7 @@
       </conditional>
       <param name="in" value="ProteinQuantifier_input.consensusXML"/>
       <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="mztab" file="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
       <param name="top" value="3"/>
       <param name="average" value="sum"/>
       <param name="include_all" value="true"/>
@@ -23832,7 +24686,7 @@
         <param name="quoting" value="double"/>
         <param name="replacement" value="_"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mztab_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -24047,9 +24901,9 @@
         <param name="tolerance" value="20.0"/>
       </section>
       <section name="MS2_id_rate">
-        <param name="force_no_fdr" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_cm_FLAG"/>
+        <param name="assume_all_target" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_cm_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -24570,6 +25424,7 @@
       <output name="out" file="SimpleSearchEngine_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
       <section name="Search">
         <param name="enzyme" value="Trypsin"/>
+        <param name="decoys" value="false"/>
         <section name="precursor">
           <param name="mass_tolerance" value="5.0"/>
           <param name="mass_tolerance_unit" value="ppm"/>
@@ -24586,6 +25441,9 @@
           <param name="variable" value="Oxidation (M)"/>
           <param name="variable_max_per_peptide" value="2"/>
         </section>
+        <section name="annotate">
+          <param name="PSM" value=""/>
+        </section>
         <section name="peptide">
           <param name="min_size" value="7"/>
           <param name="max_size" value="40"/>
@@ -24635,7 +25493,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="true"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -24679,7 +25536,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="true"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -24723,7 +25579,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="true"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -24767,7 +25622,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -24811,7 +25665,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -24855,7 +25708,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -24892,7 +25744,7 @@
       <section name="sirius">
         <param name="profile" value="qtof"/>
         <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
+        <param name="database" value="pubchem"/>
         <param name="noise" value="0"/>
         <param name="ppm_max" value="10"/>
         <param name="isotope" value="both"/>
@@ -24900,7 +25752,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="true"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -25035,6 +25886,8 @@
   <xml name="autotest_SpectraMerger">
 </xml>
   <xml name="autotest_SpectraSTSearchAdapter"/>
+  <xml name="autotest_StaticModification">
+</xml>
   <xml name="autotest_SvmTheoreticalSpectrumGeneratorTrainer">
 </xml>
   <xml name="autotest_TargetedFileConverter">
@@ -25487,7 +26340,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_1_input.featureXML"/>
-      <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25510,7 +26363,7 @@
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25524,7 +26377,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_2_input.consensusXML"/>
-      <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25550,7 +26403,7 @@
       <output name="consensus_centroids" file="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta="5700" ftype="csv"/>
       <output name="consensus_elements" file="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta="5700" ftype="csv"/>
       <output name="consensus_features" file="TextExporter_2_consensus_features.tmp" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25564,7 +26417,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_3_input.idXML"/>
-      <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25587,7 +26440,7 @@
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25601,7 +26454,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_3_input.idXML"/>
-      <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25624,7 +26477,7 @@
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25638,7 +26491,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_5_input.idXML"/>
-      <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25661,7 +26514,7 @@
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25675,7 +26528,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_6_input.featureXML"/>
-      <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25698,7 +26551,7 @@
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25712,7 +26565,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_7_input.consensusXML"/>
-      <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25735,7 +26588,7 @@
         <param name="sort_by_maps" value="true"/>
         <param name="sort_by_size" value="true"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25749,7 +26602,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_1_input.featureXML"/>
-      <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25772,7 +26625,7 @@
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25786,7 +26639,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_9_input.idXML"/>
-      <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25809,7 +26662,7 @@
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25909,8 +26762,8 @@
       <param name="in" value="TOFCalibration_1_input.mzML"/>
       <output name="out" file="TOFCalibration_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
       <param name="ext_calibrants" value="TOFCalibration_1_calibrants.mzML"/>
-      <param name="ref_masses" value="TOFCalibration_ref_masses.txt" ftype="txt"/>
-      <param name="tof_const" value="TOFCalibration_const.csv" ftype="csv"/>
+      <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>
+      <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>
       <param name="peak_data" value="false"/>
       <section name="algorithm">
         <section name="PeakPicker">
@@ -25991,8 +26844,8 @@
       <param name="in" value="TOFCalibration_2_input.mzML"/>
       <output name="out" file="TOFCalibration_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
       <param name="ext_calibrants" value="TOFCalibration_2_calibrants.mzML"/>
-      <param name="ref_masses" value="TOFCalibration_ref_masses.txt" ftype="txt"/>
-      <param name="tof_const" value="TOFCalibration_const.csv" ftype="csv"/>
+      <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>
+      <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>
       <param name="peak_data" value="true"/>
       <section name="algorithm">
         <section name="PeakPicker">
@@ -26316,5 +27169,37 @@
         </assert_contents>
       </output>
     </test>
-  </xml>
-<xml name="autotest_InspectAdapter"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_IDDecoyProbability"/><xml name="autotest_RTPredict"/><xml name="autotest_OpenSwathDIAPreScoring"/><xml name="autotest_DigestorMotif"/><xml name="autotest_PTPredict"/></macros>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="spectra.mzML"/>
+      <output name="out" file="XTandemAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="database" value="proteinslong.fasta"/>
+      <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/>
+      <param name="ignore_adapter_param" value="false"/>
+      <param name="precursor_mass_tolerance" value="5.0"/>
+      <param name="fragment_mass_tolerance" value="0.3"/>
+      <param name="precursor_error_units" value="ppm"/>
+      <param name="fragment_error_units" value="Da"/>
+      <param name="max_precursor_charge" value="0"/>
+      <param name="no_isotope_error" value="false"/>
+      <param name="fixed_modifications" value=""/>
+      <param name="variable_modifications" value="Oxidation (M)"/>
+      <param name="minimum_fragment_mz" value="150.0"/>
+      <param name="enzyme" value="Trypsin"/>
+      <param name="missed_cleavages" value="1"/>
+      <param name="semi_cleavage" value="false"/>
+      <param name="output_results" value="all"/>
+      <param name="max_valid_expect" value="0.1"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+  </xml>
+<xml name="autotest_PTPredict"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_RTPredict"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_IDDecoyProbability"/><xml name="autotest_InspectAdapter"/></macros>
--- a/macros_test.xml	Wed Sep 23 13:43:34 2020 +0000
+++ b/macros_test.xml	Tue Oct 13 19:10:16 2020 +0000
@@ -177,20 +177,7 @@
     <output name="out" ftype="txt" value="MapStatistics2.txt"/>
   </test>
 </xml>
-<xml name="manutest_MetaboliteAdductDecharger">
-  <test expect_num_outputs="3"><!-- same input as used by Decharger -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="featurexml" value="Decharger_input.featureXML"/>
-    <output name="out_cm" ftype="consensusxml" value="MetaboliteAdductDecharger_cm.consensusXML" compare="sim_size"/>
-    <param name="OPTIONAL_OUTPUTS" value="out_fm_FLAG,outpairs_FLAG"/>
-    <output name="out_fm" ftype="featurexml" value="MetaboliteAdductDecharger_fm.featureXML" compare="sim_size"/>
-    <output name="outpairs" ftype="consensusxml" value="MetaboliteAdductDecharger_pairs.consensusXML" compare="sim_size"/>
-  </test>
-</xml>
 <xml name="manutest_MetaboliteSpectralMatcher">
-    <!-- https://github.com/OpenMS/OpenMS/issues/2078 
-        https://github.com/OpenMS/OpenMS/pull/4468-->
     <!-- same input as used in the MSGF+Adapter, should use database CHEMISTRY/MetaboliteSpectralDB.mzML -->
   <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter, used as input and database -->
     <param name="adv_opts_selector" value="advanced"/>
@@ -274,36 +261,46 @@
 </test>
 </xml>
 <xml name="manutest_OpenSwathDIAPreScoring">
-  <!-- TODO data from a test that included all the needed test files 
-       currently unusable https://github.com/OpenMS/OpenMS/pull/4443 -->
   <!-- data from a test that included all the needed test files -->
-<!--  <test>-->
-<!--    <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>-->
-<!--    <param name="swath_files" value="OpenSwathWorkflow_10.chrom.mzML.tmp"/> or OpenSwathAnalyzer_2_swathfile.mzML-->
-<!--    <output name="out" ftype="tabular" value="OpenSwathDIAPreScoring_2.tmp"/>-->
-<!--  </test>-->
+  <test>
+    <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
+    <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
+    <output_collection name="output_files" count="1">
+      <element name="OpenSwathAnalyzer_2_swathfile_mzML.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
+    </output_collection>
+  </test>
+  
+  <!-- test with two inputs (actually the same file .. symlinked) -->
+  <test>
+    <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
+    <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/>
+    <output_collection name="output_files" count="2">
+      <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
+      <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
+    </output_collection>
+  </test>
 </xml>
 <!-- adapted from macros_discarded_auto.xml (due to prefix-output)-->
 <xml name="manutest_OpenSwathFileSplitter">
-<test expect_num_outputs="3">
-  <conditional name="adv_opts_cond">
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="force" value="false"/>
-    <param name="test" value="true"/>
-  </conditional>
-  <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-  <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/>
-  <output_collection name="outputDirectory" count="6">
-    <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/>
-    <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/>
-  </output_collection>
-  <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>
-  <output name="ctd_out" ftype="xml">
-    <assert_contents>
-      <is_valid_xml/>
-    </assert_contents>
-  </output>
-</test>
+  <test expect_num_outputs="3">
+    <conditional name="adv_opts_cond">
+      <param name="adv_opts_selector" value="advanced"/>
+      <param name="force" value="false"/>
+      <param name="test" value="true"/>
+    </conditional>
+    <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
+    <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/>
+    <output_collection name="outputDirectory" count="6">
+      <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/>
+      <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/>
+    </output_collection>
+    <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>
+    <output name="ctd_out" ftype="xml">
+      <assert_contents>
+        <is_valid_xml/>
+      </assert_contents>
+    </output>
+  </test>
 </xml>
 <xml name="manutest_OpenSwathRewriteToFeatureXML">
   <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
@@ -346,7 +343,7 @@
     <param name="adv_opts_cond|adv_opts_selector" value="advanced"/>
     <param name="adv_opts_cond|skip_db_check" value="true"/>
     <param name="out_type" value="idxml"/>
-    <output name="out" ftype="idxml" value="PSMFeatureExtractor.idxml" compare="sim_size" delta="100"/>
+    <output name="out" ftype="idxml" value="PSMFeatureExtractor.idxml" compare="sim_size" delta="500"/>
   </test>
   <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
     <param name="adv_opts_cond|test" value="true"/>
@@ -355,7 +352,7 @@
     <param name="adv_opts_cond|adv_opts_selector" value="advanced"/>
     <param name="adv_opts_cond|skip_db_check" value="true"/>
     <param name="out_type" value="mzid"/>
-    <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="100" lines_diff="4"/>
+    <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="500"/>
   </test>
 </xml>
 <xml name="manutest_QCCalculator">
@@ -429,12 +426,11 @@
 </xml>
 <xml name="manutest_RTEvaluation">
   <!-- just chosen an arbitrary input and autgenerated output-->
-  <!-- https://github.com/OpenMS/OpenMS/pull/4429 -->
   <test expect_num_outputs="1">
     <param name="adv_opts_selector" value="advanced"/>
     <param name="adv_opts_cond|test" value="true"/>
     <param name="in" ftype="idxml" value="PeptideIndexer_1.idXML"/>
-    <output name="out" ftype="csv" value="RTEvaluation.tsv"/>
+    <output name="out" ftype="tabular" value="RTEvaluation.tsv"/>
   </test>
 </xml>
 <xml name="manutest_SemanticValidator">
@@ -546,4 +542,4 @@
     </output>
   </test>
 </xml>
-<xml name="manutest_IDMapper"/><xml name="manutest_ProteinQuantifier"/><xml name="manutest_PeakPickerIterative"/><xml name="manutest_FeatureLinkerUnlabeledQT"/><xml name="manutest_TICCalculator"/><xml name="manutest_IDFilter"/><xml name="manutest_IDPosteriorErrorProbability"/><xml name="manutest_FeatureFinderIdentification"/><xml name="manutest_XFDR"/><xml name="manutest_OpenSwathWorkflow"/><xml name="manutest_MassCalculator"/><xml name="manutest_IDFileConverter"/><xml name="manutest_MultiplexResolver"/><xml name="manutest_FeatureFinderSuperHirn"/><xml name="manutest_AssayGeneratorMetabo"/><xml name="manutest_MassTraceExtractor"/><xml name="manutest_SiriusAdapter"/><xml name="manutest_IDMerger"/><xml name="manutest_MSstatsConverter"/><xml name="manutest_FileMerger"/><xml name="manutest_Decharger"/><xml name="manutest_PTPredict"/><xml name="manutest_XTandemAdapter"/><xml name="manutest_FeatureFinderMetabo"/><xml name="manutest_CruxAdapter"/><xml name="manutest_OpenSwathConfidenceScoring"/><xml name="manutest_PrecursorIonSelector"/><xml name="manutest_ConsensusMapNormalizer"/><xml name="manutest_RTPredict"/><xml name="manutest_PercolatorAdapter"/><xml name="manutest_ProteinInference"/><xml name="manutest_OpenSwathDecoyGenerator"/><xml name="manutest_TextExporter"/><xml name="manutest_FeatureFinderCentroided"/><xml name="manutest_DecoyDatabase"/><xml name="manutest_SpectraFilterWindowMower"/><xml name="manutest_NoiseFilterGaussian"/><xml name="manutest_MaRaClusterAdapter"/><xml name="manutest_ConsensusID"/><xml name="manutest_FileFilter"/><xml name="manutest_InclusionExclusionListCreator"/><xml name="manutest_FeatureLinkerUnlabeledKD"/><xml name="manutest_NovorAdapter"/><xml name="manutest_OpenPepXL"/><xml name="manutest_SeedListGenerator"/><xml name="manutest_FalseDiscoveryRate"/><xml name="manutest_OpenPepXLLF"/><xml name="manutest_SpecLibSearcher"/><xml name="manutest_IDConflictResolver"/><xml name="manutest_MRMMapper"/><xml name="manutest_OMSSAAdapter"/><xml name="manutest_ExternalCalibration"/><xml name="manutest_PeakPickerHiRes"/><xml name="manutest_MascotAdapter"/><xml name="manutest_FeatureFinderMultiplex"/><xml name="manutest_MetaProSIP"/><xml name="manutest_FuzzyDiff"/><xml name="manutest_TargetedFileConverter"/><xml name="manutest_MapAlignerIdentification"/><xml name="manutest_IDRTCalibration"/><xml name="manutest_MRMTransitionGroupPicker"/><xml name="manutest_RTModel"/><xml name="manutest_OpenSwathAssayGenerator"/><xml name="manutest_IDSplitter"/><xml name="manutest_OpenSwathMzMLFileCacher"/><xml name="manutest_HighResPrecursorMassCorrector"/><xml name="manutest_OpenSwathChromatogramExtractor"/><xml name="manutest_OpenSwathAnalyzer"/><xml name="manutest_FeatureLinkerUnlabeled"/><xml name="manutest_CompNovoCID"/><xml name="manutest_DTAExtractor"/><xml name="manutest_FileInfo"/><xml name="manutest_MapAlignerSpectrum"/><xml name="manutest_IsobaricAnalyzer"/><xml name="manutest_LowMemPeakPickerHiRes"/><xml name="manutest_MyriMatchAdapter"/><xml name="manutest_InternalCalibration"/><xml name="manutest_TOFCalibration"/><xml name="manutest_MSGFPlusAdapter"/><xml name="manutest_PTModel"/><xml name="manutest_InspectAdapter"/><xml name="manutest_SpectraFilterSqrtMower"/><xml name="manutest_SimpleSearchEngine"/><xml name="manutest_PeakPickerWavelet"/><xml name="manutest_MapNormalizer"/><xml name="manutest_IDScoreSwitcher"/><xml name="manutest_FeatureLinkerLabeled"/><xml name="manutest_MapRTTransformer"/><xml name="manutest_RNPxlSearch"/><xml name="manutest_PrecursorMassCorrector"/><xml name="manutest_MapAlignerPoseClustering"/><xml name="manutest_MzTabExporter"/><xml name="manutest_BaselineFilter"/><xml name="manutest_FeatureFinderMRM"/><xml name="manutest_MascotAdapterOnline"/><xml name="manutest_DatabaseFilter"/><xml name="manutest_ProteinResolver"/><xml name="manutest_OpenSwathFeatureXMLToTSV"/><xml name="manutest_FidoAdapter"/><xml name="manutest_AccurateMassSearch"/><xml name="manutest_CompNovo"/><xml name="manutest_LowMemPeakPickerHiResRandomAccess"/><xml name="manutest_OpenSwathRTNormalizer"/><xml name="manutest_PeptideIndexer"/><xml name="manutest_CometAdapter"/><xml name="manutest_NoiseFilterSGolay"/><xml name="manutest_MSFraggerAdapter"/><xml name="manutest_SpectraSTSearchAdapter"/><xml name="manutest_SequestAdapter"/><xml name="manutest_FeatureFinder"/><xml name="manutest_LuciphorAdapter"/><xml name="manutest_GNPSExport"/><xml name="manutest_Epifany"/><xml name="manutest_NucleicAcidSearchEngine"/><xml name="manutest_QualityControl"/><xml name="manutest_FeatureFinderMetaboIdent"/><xml name="manutest_RNAMassCalculator"/><xml name="manutest_MapAlignerTreeGuided"/><xml name="manutest_IDMassAccuracy"/><xml name="manutest_ProteomicsLFQ"/><xml name="manutest_IDDecoyProbability"/><xml name="manutest_DigestorMotif"/></macros>
+<xml name="manutest_MetaboliteAdductDecharger"/><xml name="manutest_IDMapper"/><xml name="manutest_ProteinQuantifier"/><xml name="manutest_PeakPickerIterative"/><xml name="manutest_FeatureLinkerUnlabeledQT"/><xml name="manutest_TICCalculator"/><xml name="manutest_IDFilter"/><xml name="manutest_IDPosteriorErrorProbability"/><xml name="manutest_FeatureFinderIdentification"/><xml name="manutest_XFDR"/><xml name="manutest_OpenSwathWorkflow"/><xml name="manutest_MassCalculator"/><xml name="manutest_IDFileConverter"/><xml name="manutest_MultiplexResolver"/><xml name="manutest_FeatureFinderSuperHirn"/><xml name="manutest_AssayGeneratorMetabo"/><xml name="manutest_MassTraceExtractor"/><xml name="manutest_SiriusAdapter"/><xml name="manutest_IDMerger"/><xml name="manutest_MSstatsConverter"/><xml name="manutest_FileMerger"/><xml name="manutest_Decharger"/><xml name="manutest_PTPredict"/><xml name="manutest_XTandemAdapter"/><xml name="manutest_FeatureFinderMetabo"/><xml name="manutest_CruxAdapter"/><xml name="manutest_OpenSwathConfidenceScoring"/><xml name="manutest_PrecursorIonSelector"/><xml name="manutest_ConsensusMapNormalizer"/><xml name="manutest_RTPredict"/><xml name="manutest_PercolatorAdapter"/><xml name="manutest_ProteinInference"/><xml name="manutest_OpenSwathDecoyGenerator"/><xml name="manutest_TextExporter"/><xml name="manutest_FeatureFinderCentroided"/><xml name="manutest_DecoyDatabase"/><xml name="manutest_SpectraFilterWindowMower"/><xml name="manutest_NoiseFilterGaussian"/><xml name="manutest_MaRaClusterAdapter"/><xml name="manutest_ConsensusID"/><xml name="manutest_FileFilter"/><xml name="manutest_InclusionExclusionListCreator"/><xml name="manutest_FeatureLinkerUnlabeledKD"/><xml name="manutest_NovorAdapter"/><xml name="manutest_OpenPepXL"/><xml name="manutest_SeedListGenerator"/><xml name="manutest_FalseDiscoveryRate"/><xml name="manutest_OpenPepXLLF"/><xml name="manutest_SpecLibSearcher"/><xml name="manutest_IDConflictResolver"/><xml name="manutest_MRMMapper"/><xml name="manutest_OMSSAAdapter"/><xml name="manutest_ExternalCalibration"/><xml name="manutest_PeakPickerHiRes"/><xml name="manutest_MascotAdapter"/><xml name="manutest_FeatureFinderMultiplex"/><xml name="manutest_MetaProSIP"/><xml name="manutest_FuzzyDiff"/><xml name="manutest_TargetedFileConverter"/><xml name="manutest_MapAlignerIdentification"/><xml name="manutest_IDRTCalibration"/><xml name="manutest_MRMTransitionGroupPicker"/><xml name="manutest_RTModel"/><xml name="manutest_OpenSwathAssayGenerator"/><xml name="manutest_IDSplitter"/><xml name="manutest_OpenSwathMzMLFileCacher"/><xml name="manutest_HighResPrecursorMassCorrector"/><xml name="manutest_OpenSwathChromatogramExtractor"/><xml name="manutest_OpenSwathAnalyzer"/><xml name="manutest_FeatureLinkerUnlabeled"/><xml name="manutest_CompNovoCID"/><xml name="manutest_DTAExtractor"/><xml name="manutest_FileInfo"/><xml name="manutest_MapAlignerSpectrum"/><xml name="manutest_IsobaricAnalyzer"/><xml name="manutest_LowMemPeakPickerHiRes"/><xml name="manutest_MyriMatchAdapter"/><xml name="manutest_InternalCalibration"/><xml name="manutest_TOFCalibration"/><xml name="manutest_MSGFPlusAdapter"/><xml name="manutest_PTModel"/><xml name="manutest_InspectAdapter"/><xml name="manutest_SpectraFilterSqrtMower"/><xml name="manutest_SimpleSearchEngine"/><xml name="manutest_PeakPickerWavelet"/><xml name="manutest_MapNormalizer"/><xml name="manutest_IDScoreSwitcher"/><xml name="manutest_FeatureLinkerLabeled"/><xml name="manutest_MapRTTransformer"/><xml name="manutest_RNPxlSearch"/><xml name="manutest_PrecursorMassCorrector"/><xml name="manutest_MapAlignerPoseClustering"/><xml name="manutest_MzTabExporter"/><xml name="manutest_BaselineFilter"/><xml name="manutest_FeatureFinderMRM"/><xml name="manutest_MascotAdapterOnline"/><xml name="manutest_DatabaseFilter"/><xml name="manutest_ProteinResolver"/><xml name="manutest_OpenSwathFeatureXMLToTSV"/><xml name="manutest_FidoAdapter"/><xml name="manutest_AccurateMassSearch"/><xml name="manutest_CompNovo"/><xml name="manutest_LowMemPeakPickerHiResRandomAccess"/><xml name="manutest_OpenSwathRTNormalizer"/><xml name="manutest_PeptideIndexer"/><xml name="manutest_CometAdapter"/><xml name="manutest_NoiseFilterSGolay"/><xml name="manutest_MSFraggerAdapter"/><xml name="manutest_SpectraSTSearchAdapter"/><xml name="manutest_SequestAdapter"/><xml name="manutest_FeatureFinder"/><xml name="manutest_LuciphorAdapter"/><xml name="manutest_GNPSExport"/><xml name="manutest_Epifany"/><xml name="manutest_NucleicAcidSearchEngine"/><xml name="manutest_QualityControl"/><xml name="manutest_FeatureFinderMetaboIdent"/><xml name="manutest_RNAMassCalculator"/><xml name="manutest_MapAlignerTreeGuided"/><xml name="manutest_IDMassAccuracy"/><xml name="manutest_ProteomicsLFQ"/><xml name="manutest_IDDecoyProbability"/><xml name="manutest_DigestorMotif"/><xml name="manutest_DatabaseSuitability"/><xml name="manutest_StaticModification"/></macros>
--- a/prepare_test_data.sh	Wed Sep 23 13:43:34 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1196 +0,0 @@
-export COMET_BINARY="comet"
-export CRUX_BINARY="crux"
-export FIDOCHOOSEPARAMS_BINARY="FidoChooseParameters"
-export FIDO_BINARY="Fido"
-export LUCIPHOR_BINARY="$(dirname $(realpath $(which luciphor2)))/luciphor2.jar"
-export MARACLUSTER_BINARY="/tmp/openms-stuff//OpenMS2.5.0-git/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster"
-export MSFRAGGER_BINARY="/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar"
-export MSGFPLUS_BINARY="$(msgf_plus -get_jar_path)"
-export MYRIMATCH_BINARY="myrimatch"
-export NOVOR_BINARY="/home/berntm/Downloads/novor/lib/novor.jar"
-export OMSSA_BINARY="$(dirname $(realpath $(which omssacl)))/omssacl"
-export PERCOLATOR_BINARY="percolator"
-export SIRIUS_BINARY="$(which sirius)"
-export SPECTRAST_BINARY="spectrast"
-export XTANDEM_BINARY="xtandem"
-export THERMORAWFILEPARSER_BINARY="ThermoRawFileParser.exe"
-FuzzyDiff -test -ini FuzzyDiff.ini -in1 FuzzyDiff_3_in1.featureXML -in2 FuzzyDiff_3_in2.featureXML > UTILS_FuzzyDiff_3.stdout 2> UTILS_FuzzyDiff_3.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_FuzzyDiff_3 failed'; >&2 echo -e "stderr:\n$(cat UTILS_FuzzyDiff_3.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat UTILS_FuzzyDiff_3.stdout)";fi
-IDMerger -test -in IDMerger_1_input1.idXML IDMerger_1_input2.idXML -out IDMerger_1_output.tmp -annotate_file_origin > TOPP_IDMerger_1.stdout 2> TOPP_IDMerger_1.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMerger_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMerger_1.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_IDMerger_1.stdout)";fi
-IDMerger -test -pepxml_protxml -in IDMerger_2_input1.idXML IDMerger_2_input2.idXML -out IDMerger_2_output.tmp > TOPP_IDMerger_2.stdout 2> TOPP_IDMerger_2.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMerger_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMerger_2.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_IDMerger_2.stdout)";fi
-IDMerger -test -in IDMerger_1_input1.idXML IDMerger_1_input1.idXML -out IDMerger_3_output.tmp > TOPP_IDMerger_3.stdout 2> TOPP_IDMerger_3.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMerger_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMerger_3.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_IDMerger_3.stdout)";fi
-IDMerger -test -in degenerated_empty.idXML degenerated_empty.idXML -out IDMerger_4_output.tmp > TOPP_IDMerger_4.stdout 2> TOPP_IDMerger_4.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMerger_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMerger_4.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_IDMerger_4.stdout)";fi
-IDMerger -test -in IDMerger_2_input1.idXML -add_to IDMerger_5_input1.idXML -out IDMerger_5_output.tmp > TOPP_IDMerger_5.stdout 2> TOPP_IDMerger_5.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMerger_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMerger_5.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_IDMerger_5.stdout)";fi
-BaselineFilter -test -in BaselineFilter_input.mzML -out BaselineFilter.tmp -struc_elem_length 1.5 > TOPP_BaselineFilter_1.stdout 2> TOPP_BaselineFilter_1.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_BaselineFilter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_BaselineFilter_1.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_BaselineFilter_1.stdout)";fi
-ConsensusMapNormalizer -test -in ConsensusMapNormalizer_input.consensusXML -out ConsensusMapNormalizer.tmp > TOPP_ConsensusMapNormalizer_1.stdout 2> TOPP_ConsensusMapNormalizer_1.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConsensusMapNormalizer_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConsensusMapNormalizer_1.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_ConsensusMapNormalizer_1.stdout)";fi
-MapNormalizer -test -in MapNormalizer_input.mzML -out MapNormalizer.tmp > TOPP_MapNormalizer_1.stdout 2> TOPP_MapNormalizer_1.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapNormalizer_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapNormalizer_1.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_MapNormalizer_1.stdout)";fi
-Decharger -test -in Decharger_input.featureXML -ini Decharger_input.ini -out_fm Decharger_output_fm.tmp -out_cm Decharger_output.tmp -outpairs Decharger_p_output.tmp > TOPP_Decharger_1.stdout 2> TOPP_Decharger_1.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_Decharger_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_Decharger_1.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_Decharger_1.stdout)";fi
-DTAExtractor -test -in DTAExtractor_1_input.mzML -out DTAExtractor -rt :61 > TOPP_DTAExtractor_1.stdout 2> TOPP_DTAExtractor_1.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_DTAExtractor_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_DTAExtractor_1.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_DTAExtractor_1.stdout)";fi
-DTAExtractor -test -in DTAExtractor_1_input.mzML -out DTAExtractor -level 1 > TOPP_DTAExtractor_2.stdout 2> TOPP_DTAExtractor_2.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_DTAExtractor_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_DTAExtractor_2.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_DTAExtractor_2.stdout)";fi
-DTAExtractor -test -in DTAExtractor_1_input.mzML -out DTAExtractor -level 2 -mz :1000 > TOPP_DTAExtractor_3.stdout 2> TOPP_DTAExtractor_3.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_DTAExtractor_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_DTAExtractor_3.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_DTAExtractor_3.stdout)";fi
-MassTraceExtractor -test -ini MassTraceExtractor.ini -in MassTraceExtractor_1_input.mzML -out MassTraceExtractor_1.tmp > TOPP_MassTraceExtractor_1.stdout 2> TOPP_MassTraceExtractor_1.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MassTraceExtractor_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MassTraceExtractor_1.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_MassTraceExtractor_1.stdout)";fi
-MassTraceExtractor -test -ini MassTraceExtractor_2.ini -in MassTraceExtractor_1_input.mzML -out MassTraceExtractor_2.tmp > TOPP_MassTraceExtractor_2.stdout 2> TOPP_MassTraceExtractor_2.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MassTraceExtractor_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MassTraceExtractor_2.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_MassTraceExtractor_2.stdout)";fi
-FeatureFinderMetabo -test -ini FeatureFinderMetabo.ini -in FeatureFinderMetabo_1_input.mzML -out FeatureFinderMetabo_1.tmp > TOPP_FeatureFinderMetabo_1.stdout 2> TOPP_FeatureFinderMetabo_1.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMetabo_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMetabo_1.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMetabo_1.stdout)";fi
-FeatureFinderMetabo -test -ini FeatureFinderMetabo_2_noEPD.ini -in FeatureFinderMetabo_2_input.mzML -out FeatureFinderMetabo_2.tmp > TOPP_FeatureFinderMetabo_2.stdout 2> TOPP_FeatureFinderMetabo_2.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMetabo_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMetabo_2.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMetabo_2.stdout)";fi
-FeatureFinderMetabo -test -ini FeatureFinderMetabo_3.ini -in FeatureFinderMetabo_3_input.mzML -out FeatureFinderMetabo_3.tmp -out_chrom FeatureFinderMetabo_3_chrom.tmp > TOPP_FeatureFinderMetabo_3.stdout 2> TOPP_FeatureFinderMetabo_3.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMetabo_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMetabo_3.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMetabo_3.stdout)";fi
-FeatureFinderMetabo -test -ini FeatureFinderMetabo_4.ini -in FeatureFinderMetabo_3_input.mzML -out FeatureFinderMetabo_4.tmp -out_chrom FeatureFinderMetabo_4_chrom.tmp > TOPP_FeatureFinderMetabo_4.stdout 2> TOPP_FeatureFinderMetabo_4.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMetabo_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMetabo_4.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMetabo_4.stdout)";fi
-FeatureFinderMetabo -test -ini FeatureFinderMetabo.ini -in FeatureFinderMetabo_1_input.mzML -out FeatureFinderMetabo_5.tmp -algorithm:mtd:quant_method max_height > TOPP_FeatureFinderMetabo_5.stdout 2> TOPP_FeatureFinderMetabo_5.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMetabo_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMetabo_5.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMetabo_5.stdout)";fi
-FeatureFinderCentroided -test -ini FeatureFinderCentroided_1_parameters.ini -in FeatureFinderCentroided_1_input.mzML -out FeatureFinderCentroided_1.tmp > TOPP_FeatureFinderCentroided_1.stdout 2> TOPP_FeatureFinderCentroided_1.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderCentroided_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderCentroided_1.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderCentroided_1.stdout)";fi
-FeatureFinderIdentification -test -in FeatureFinderIdentification_1_input.mzML -id FeatureFinderIdentification_1_input.idXML -out FeatureFinderIdentification_1.tmp -extract:mz_window 0.1 -detect:peak_width 60 -model:type none > TOPP_FeatureFinderIdentification_1.stdout 2> TOPP_FeatureFinderIdentification_1.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderIdentification_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderIdentification_1.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderIdentification_1.stdout)";fi
-FeatureFinderIdentification -test -in FeatureFinderIdentification_1_input.mzML -id FeatureFinderIdentification_1_input.idXML -out FeatureFinderIdentification_3.tmp -extract:mz_window 0.1 -detect:peak_width 60 -model:type symmetric > TOPP_FeatureFinderIdentification_3.stdout 2> TOPP_FeatureFinderIdentification_3.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderIdentification_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderIdentification_3.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderIdentification_3.stdout)";fi
-FeatureFinderIdentification -test -in FeatureFinderIdentification_1_input.mzML -id FeatureFinderIdentification_1_input.idXML -out FeatureFinderIdentification_4.tmp -extract:mz_window 0.1 -extract:batch_size 10 -detect:peak_width 60 -model:type none > TOPP_FeatureFinderIdentification_4.stdout 2> TOPP_FeatureFinderIdentification_4.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderIdentification_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderIdentification_4.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderIdentification_4.stdout)";fi
-FeatureFinderMRM -test -in FeatureFinderMRM_1_input.mzML -ini FeatureFinderMRM_1_parameters.ini -out FeatureFinderMRM_1.tmp > TOPP_FeatureFinderMRM_1.stdout 2> TOPP_FeatureFinderMRM_1.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMRM_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMRM_1.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMRM_1.stdout)";fi
-FeatureFinderMultiplex -test -in FeatureFinderMultiplex_1_input.mzML -ini FeatureFinderMultiplex_1_parameters.ini -out FeatureFinderMultiplex_1.tmp -out_multiplets FeatureFinderMultiplex_2.tmp > TOPP_FeatureFinderMultiplex_1.stdout 2> TOPP_FeatureFinderMultiplex_1.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_1.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_1.stdout)";fi
-FeatureFinderMultiplex -test -in FeatureFinderMultiplex_2_input.mzML -ini FeatureFinderMultiplex_2_parameters.ini -out FeatureFinderMultiplex_3.tmp -out_multiplets FeatureFinderMultiplex_4.tmp > TOPP_FeatureFinderMultiplex_2.stdout 2> TOPP_FeatureFinderMultiplex_2.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_2.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_2.stdout)";fi
-FeatureFinderMultiplex -test -in FeatureFinderMultiplex_3_input.mzML -ini FeatureFinderMultiplex_3_parameters.ini -out FeatureFinderMultiplex_5.tmp -out_multiplets FeatureFinderMultiplex_6.tmp > TOPP_FeatureFinderMultiplex_3.stdout 2> TOPP_FeatureFinderMultiplex_3.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_3.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_3.stdout)";fi
-FeatureFinderMultiplex -test -in FeatureFinderMultiplex_4_input.mzML -ini FeatureFinderMultiplex_4_parameters.ini -out FeatureFinderMultiplex_7.tmp -out_multiplets FeatureFinderMultiplex_8.tmp > TOPP_FeatureFinderMultiplex_4.stdout 2> TOPP_FeatureFinderMultiplex_4.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_4.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_4.stdout)";fi
-FeatureFinderMultiplex -test -in FeatureFinderMultiplex_5_input.mzML -ini FeatureFinderMultiplex_5_parameters.ini -out FeatureFinderMultiplex_9.tmp -out_multiplets FeatureFinderMultiplex_10.tmp > TOPP_FeatureFinderMultiplex_5.stdout 2> TOPP_FeatureFinderMultiplex_5.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_5.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_5.stdout)";fi
-FeatureFinderMultiplex -test -in FeatureFinderMultiplex_6_input.mzML -ini FeatureFinderMultiplex_6_parameters.ini -out FeatureFinderMultiplex_11.tmp -out_multiplets FeatureFinderMultiplex_12.tmp > TOPP_FeatureFinderMultiplex_6.stdout 2> TOPP_FeatureFinderMultiplex_6.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_6.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_6.stdout)";fi
-FeatureFinderMultiplex -test -in FeatureFinderMultiplex_7_input.mzML -ini FeatureFinderMultiplex_7_parameters.ini -out FeatureFinderMultiplex_13.tmp -out_multiplets FeatureFinderMultiplex_14.tmp > TOPP_FeatureFinderMultiplex_7.stdout 2> TOPP_FeatureFinderMultiplex_7.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_7.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_7.stdout)";fi
-FeatureFinderMultiplex -test -in FeatureFinderMultiplex_8_input.mzML -ini FeatureFinderMultiplex_8_parameters.ini -out FeatureFinderMultiplex_15.tmp -out_multiplets FeatureFinderMultiplex_16.tmp > TOPP_FeatureFinderMultiplex_8.stdout 2> TOPP_FeatureFinderMultiplex_8.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_8.stderr | sed 's/^/    /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_8.stdout)";fi
-FeatureFinderMultiplex -test -in FeatureFinderMultiplex_9_input.mzML -ini FeatureFinderMultiplex_9_parameters.ini -out FeatureFinderMultiplex_17.tmp -out_multiplets FeatureFinderMultiplex_18.tmp > TOPP_FeatureFinderMultiplex_9.stdout 2> TOPP_FeatureFinderMultiplex_9.stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_9 failed'; &