Mercurial > repos > bgruening > peptideshaker
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--- a/README.md Mon Dec 15 21:33:25 2014 -0500 +++ b/README.md Mon Feb 16 04:18:17 2015 -0500 @@ -1,10 +1,9 @@ GalaxyP - PeptideShaker ======================= -* Home: <https://bitbucket.org/galaxyp/peptideshaker> +* Home: <https://github.com/galaxyproteomics/tools-galaxyp/> * Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/peptideshaker> -* Tool ID: `peptideshaker` -* Tool Type: `default` +* Tool ID: `peptideshaker`, `search_gui` Description @@ -14,19 +13,18 @@ Tool wrapper for SearchGUI and PeptideShaker. This tool takes any number of mgf files and performs X! Tandem and OMSSA searches on these via SearchGUI and merges the results using PeptideShaker. + Configuration ------------- -This tool requires a Java runtime 1.6 or greater to work. To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell; +This tool requires a Java runtime 1.6 or greater to work. To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell: -export _JAVA_OPTIONS='-Xmx1500M' + export _JAVA_OPTIONS='-Xmx1500M' -It is also possible to set this on a per tool basis using advanced features of the galaxy job config system +It is also possible to set this on a per tool basis using advanced features of the galaxy job config system. Note: -- SearchGUI requires a version greater than 1.12.2 which contained several bugs preventing this from working on the command-line and via Linux. - - PeptideShaker may require xvfb to simulate an X environment if this is installed on a headless server. See: @@ -38,9 +36,9 @@ GalaxyP Community ----------------- -Current governing community policies for [GalaxyP](https://bitbucket.org/galaxyp/) and other information can be found at: +Current governing community policies for [GalaxyP](https://github.com/galaxyproteomics/) and other information can be found at: -<https://bitbucket.org/galaxyp/galaxyp> +<https://github.com/galaxyproteomics> License @@ -58,7 +56,7 @@ Contributing ------------ -Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://bitbucket.org/galaxyp/galaxyp/CONTRIBUTORS.md> unless you opt-out. +Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://github.com/galaxyproteomics/tools-galaxyp/> Authors
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Mon Feb 16 04:18:17 2015 -0500 @@ -0,0 +1,7 @@ +<?xml version="1.0"?> +<datatypes> + <registration> + <datatype extension="searchgui_zip" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /> + <datatype extension="peptideshaker_zip" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /> + </registration> +</datatypes>
--- a/macros.xml Mon Dec 15 21:33:25 2014 -0500 +++ b/macros.xml Mon Feb 16 04:18:17 2015 -0500 @@ -98,6 +98,7 @@ <citations> <citation type="doi">10.1186/1471-2105-12-70</citation> <citation type="doi">10.1002/pmic.201000595</citation> + <citation type="doi">doi:10.1038/nbt.3109</citation> </citations> </xml>
--- a/peptide_shaker.xml Mon Dec 15 21:33:25 2014 -0500 +++ b/peptide_shaker.xml Mon Feb 16 04:18:17 2015 -0500 @@ -1,40 +1,36 @@ -<tool id="peptide_shaker" name="Peptide Shaker" version="1.35.0"> +<tool id="peptide_shaker" name="Peptide Shaker" version="0.37.0"> <description> Perform protein identification using various search engines based on results from SearchGUI </description> <requirements> - <requirement type="package" version="0.35">peptide_shaker</requirement> + <requirement type="package" version="0.37">peptide_shaker</requirement> </requirements> - + <macros> + <import>macros.xml</import> + </macros> <expand macro="stdio" /> <command> <![CDATA[ - - ######################################################### - ## generate IdentificationParameters for PeptideShaker ## - ######################################################### - (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.IdentificationParametersCLI - -out PEPTIDESHAKER_IdentificationParameters.parameters + #from datetime import datetime + #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s") + #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s") + #set $temp_stderr = "peptideshaker_stderr" - @GENERAL_PARAMETERS@ - - -db input_database.fasta + mkdir output_reports; + cwd=`pwd`; - 2>> $temp_stderr) - && - + ln -s '$searchgui_input' searchgui_input.zip && ###################### ## PeptideShakerCLI ## ###################### (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI -temp_folder `pwd` - -experiment '${exp_str}' - -sample '${samp_str}' + -experiment '$exp_str' + -sample '$samp_str' -replicate 1 - -spectrum_files \$cwd - -identification_files \$cwd/output - -out \$cwd/peptide_shaker_output.cps - -id_params PEPTIDESHAKER_IdentificationParameters.parameters + -identification_files \$cwd/searchgui_input.zip + -out \$cwd/peptideshaker_output.cps + -zip \$cwd/peptideshaker_output.zip -threads "\${GALAXY_SLOTS:-12}" @@ -42,6 +38,7 @@ #if $species_type.species_type_selector != 'no_species_type': -species_type "${species_type.species_type_selector}" -species "${species_type.species}" + -species_update 1 #end if ##Optional processing parameters: @@ -65,37 +62,26 @@ -max_peptide_length "${filtering_options.max_peptide_length}" -max_precursor_error "${filtering_options.max_precursor_error}" -max_precursor_error_type "${filtering_options.max_precursor_error_type}" - -max_xtandem_e "${filtering_options.max_xtandem_e}" - -max_omssa_e "${filtering_options.max_omssa_e}" - -max_mascot_e "${filtering_options.max_mascot_e}" + ##-max_xtandem_e "${filtering_options.max_xtandem_e}" + ##-max_omssa_e "${filtering_options.max_omssa_e}" + ##-max_mascot_e "${filtering_options.max_mascot_e}" -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}" #end if 2>> $temp_stderr) + && + echo "Running Reports"; + ################################## ## PeptideShaker Report options ## ################################## - (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.ReportCLI - -temp_folder `pwd` - -in \$cwd/peptide_shaker_output.cps - -out_reports \$cwd/output_reports - #set $cleaned_list = str($outputs).split(',') - #if 'cps' in $cleaned_list: - #silent $cleaned_list.remove('cps') - #end if - #if 'mzidentML' in $cleaned_list: - #silent $cleaned_list.remove('mzidentML') - #end if - -reports #echo ','.join($cleaned_list)# - - 2>> $temp_stderr) - && #if 'mzidentML' in str($outputs).split(','): - java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.MzidCLI - -in \$cwd/peptide_shaker_output.cps + echo "Generating mzIdentML"; + (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.MzidCLI + -in \$cwd/peptideshaker_output.zip -output_file output.mzid -contact_first_name 'Proteomics' -contact_last_name 'Galaxy' @@ -104,58 +90,81 @@ -organization_name 'University of Minnesota' -organization_email 'galaxyp@umn.edu' -organization_address 'Minneapolis, MN 55455, Vereinigte Staaten' - ; - #end if - #if '0' in str($outputs).split(','): - find \$cwd/output_reports -name '*Certificate*' -exec bash -c 'mv "$0" "certificate.txt"' {} \; - ; + 2>> $temp_stderr) + && #end if - #if '2' in str($outputs).split(','): - find \$cwd/output_reports -name '*PSM*' -exec bash -c 'mv "$0" "psm.txt"' {} \; - ; + + ## Generate Reports if the user has selected one of the 8 additional reports + ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker + ## and will not be passed to the command line + #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ): + + (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.ReportCLI + -temp_folder `pwd` + -in \$cwd/peptideshaker_output.zip + -out_reports \$cwd/output_reports + #set $cleaned_list = str($outputs).split(',') + #if 'cps' in $cleaned_list: + #silent $cleaned_list.remove('cps') + #end if + #if 'mzidentML' in $cleaned_list: + #silent $cleaned_list.remove('mzidentML') + #end if + #if 'zip' in $cleaned_list: + #silent $cleaned_list.remove('zip') + #end if + ## Only numbers are left over. These corresponds to different reports. + -reports #echo ','.join($cleaned_list)# + + 2>> $temp_stderr) + && #end if - #if '3' in str($outputs).split(','): - find \$cwd/output_reports -name '*Peptide*' -exec bash -c 'mv "$0" "peptides.txt"' {} \; - ; - #end if - #if '4' in str($outputs).split(','): - find \$cwd/output_reports -name '*Protein*' -exec bash -c 'mv "$0" "proteins.txt"' {} \; + + + #if '0' in str($outputs).split(','): + find \$cwd/output_reports -name '*Certificate_of_Analysis*' -exec bash -c 'mv "$0" "certificate.txt"' {} \; ; #end if #if '1' in str($outputs).split(','): find \$cwd/output_reports -name '*Hierarchical*' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \; ; #end if + #if '2' in str($outputs).split(','): + find \$cwd/output_reports -name '*PSM_Phosphorylation_Report*' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \; + ; + #end if + #if '3' in str($outputs).split(','): + find \$cwd/output_reports -name '*PSM_Report*' -exec bash -c 'mv "$0" "psm.txt"' {} \; + ; + #end if + #if '4' in str($outputs).split(','): + find \$cwd/output_reports -name '*Peptide_Phosphorylation_Report*' -exec bash -c 'mv "$0" "peptides_phospho.txt"' {} \; + ; + #end if + #if '5' in str($outputs).split(','): + find \$cwd/output_reports -name '*Peptide_Report*' -exec bash -c 'mv "$0" "peptides.txt"' {} \; + ; + #end if + #if '6' in str($outputs).split(','): + find \$cwd/output_reports -name '*Protein_Phosphorylation_Report*' -exec bash -c 'mv "$0" "proteins_phospho.txt"' {} \; + ; + #end if + #if '7' in str($outputs).split(','): + find \$cwd/output_reports -name '*Protein_Report*' -exec bash -c 'mv "$0" "proteins.txt"' {} \; + ; + #end if exit_code_for_galaxy=\$?; - cat $temp_stderr 2>&1; + cat $temp_stderr 2>&1; (exit \$exit_code_for_galaxy) + + && cp * /home/bag/arg -R + ]]> </command> <inputs> - <param format="fasta" name="input_database" type="data" label="Protein Database" - help="Select FASTA database from history"/> - - <param name="create_decoy" label="Create a concatenated target/decoy database before running PeptideShaker." type="boolean" truevalue="True" falsevalue="False" checked="true" help="Selecting this option will help PeptideShaker calculate FDR values" /> - - <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)" - help="Select appropriate MGF dataset(s) from history" /> - - <expand macro="general_options"/> - - <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?" - help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option"> - <option value="0">no correction</option> - <option value="1" selected="True">rename spectra</option> - <option value="2">delete spectra</option> - </param> - - <param name="missing_titles" label="Add missing spectrum titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0" help="(-missing_titles)"/> - - <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf" - help="Choose a smaller value if you are running on a machine with limited memory"/> - <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting" - help="Choose a smaller value if you are running on a machine with limited memory"/> + <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results" + help="SearchGUI Results from History"/> <conditional name="species_type"> <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation" @@ -171,14 +180,20 @@ <param name="species" type="select" label="The species to use for the gene annotation" help=""> <option value="Albugo laibachii">Albugo laibachii</option> + <option value="Bigelowiella natans">Bigelowiella natans</option> <option value="Dictyostelium discoideum">Dictyostelium discoideum</option> + <option value="Emiliania huxleyi">Emiliania huxleyi</option> <option value="Entamoeba histolytica">Entamoeba histolytica</option> <option value="Giardia lamblia">Giardia lamblia</option> <option value="Guillardia theta CCMP2712">Guillardia theta CCMP2712</option> <option value="Hyaloperonospora arabidopsidis">Hyaloperonospora arabidopsidis</option> <option value="Leishmania major">Leishmania major</option> + <option value="Paramecium tetraurelia">Paramecium tetraurelia</option> <option value="Phaeodactylum tricornutum">Phaeodactylum tricornutum</option> <option value="Phytophthora infestans">Phytophthora infestans</option> + <option value="Phytophthora kernoviae">Phytophthora kernoviae</option> + <option value="Phytophthora lateralis">Phytophthora lateralis</option> + <option value="Phytophthora parasitica">Phytophthora parasitica</option> <option value="Phytophthora ramorum">Phytophthora ramorum</option> <option value="Phytophthora sojae">Phytophthora sojae</option> <option value="Plasmodium berghei">Plasmodium berghei</option> @@ -186,7 +201,12 @@ <option value="Plasmodium falciparum">Plasmodium falciparum</option> <option value="Plasmodium knowlesi">Plasmodium knowlesi</option> <option value="Plasmodium vivax">Plasmodium vivax</option> + <option value="Pythium aphanidermatum">Pythium aphanidermatum</option> + <option value="Pythium arrhenomanes">Pythium arrhenomanes</option> + <option value="Pythium irregulare">Pythium irregulare</option> + <option value="Pythium iwayamai">Pythium iwayamai</option> <option value="Pythium ultimum">Pythium ultimum</option> + <option value="Pythium vexans">Pythium vexans</option> <option value="Tetrahymena thermophila">Tetrahymena thermophila</option> <option value="Thalassiosira pseudonana">Thalassiosira pseudonana</option> <option value="Toxoplasma gondii">Toxoplasma gondii</option> @@ -196,77 +216,102 @@ <when value="Plants"> <param name="species" type="select" label="The species to use for the gene annotation" help=""> - <option value="Arabidopsis lyrata">Arabidopsis lyrata</option> - <option value="Arabidopsis thaliana">Arabidopsis thaliana</option> - <option value="Brachypodium distachyon">Brachypodium distachyon</option> - <option value="Brassica rapa genes">Brassica rapa genes</option> - <option value="Chlamydomonas reinhardtii">Chlamydomonas reinhardtii</option> - <option value="Cyanidioschyzon merolae">Cyanidioschyzon merolae</option> - <option value="Glycine max">Glycine max</option> - <option value="Hordeum vulgare">Hordeum vulgare</option> - <option value="Medicago truncatula">Medicago truncatula</option> - <option value="Musa acuminata">Musa acuminata</option> + <option value="Amborella (Amborella trichopoda)">Amborella (Amborella trichopoda)</option> + <option value="Arabidopsis lyrata (Lyrate rockcress)">Arabidopsis lyrata (Lyrate rockcress)</option> + <option value="Arabidopsis thaliana (Thale-cress)">Arabidopsis thaliana (Thale-cress)</option> + <option value="Brachypodium distachyon (False brome)">Brachypodium distachyon (False brome)</option> + <option value="Brassica oleracea">Brassica oleracea</option> + <option value="Brassica rapa genes (Field mustard)">Brassica rapa genes (Field mustard)</option> + <option value="Chlamydomonas reinhardtii (Green algae)">Chlamydomonas reinhardtii (Green algae)</option> + <option value="Cyanidioschyzon merolae (Red algae)">Cyanidioschyzon merolae (Red algae)</option> + <option value="Glycine max (Soybean)">Glycine max (Soybean)</option> + <option value="Hordeum vulgare (Barley)">Hordeum vulgare (Barley)</option> + <option value="Leersia perrieri (Leersia)">Leersia perrieri (Leersia)</option> + <option value="Medicago truncatula (Barrel medic)">Medicago truncatula (Barrel medic)</option> + <option value="Musa acuminata (Banana)">Musa acuminata (Banana)</option> <option value="Oryza brachyantha">Oryza brachyantha</option> - <option value="Oryza glaberrima">Oryza glaberrima</option> + <option value="Oryza glumaepatula">Oryza glumaepatula</option> + <option value="Oryza meridionalis">Oryza meridionalis</option> + <option value="Oryza nivara">Oryza nivara</option> + <option value="Oryza punctata">Oryza punctata</option> + <option value="Oryza rufipogon (Common wild rice)">Oryza rufipogon (Common wild rice)</option> + <option value="Oryza sativa (Indica rice)">Oryza sativa (Indica rice)</option> <option value="Oryza sativa Indica Group">Oryza sativa Indica Group</option> - <option value="Oryza sativa">Oryza sativa</option> + <option value="Oryza sativa Japonica (Japonica rice)">Oryza sativa Japonica (Japonica rice)</option> + <option value="Ostreococcus lucimarinus (Green algae)">Ostreococcus lucimarinus (Green algae)</option> <option value="Physcomitrella patens">Physcomitrella patens</option> + <option value="Physcomitrella patens (Moss)">Physcomitrella patens (Moss)</option> <option value="Populus trichocarpa">Populus trichocarpa</option> - <option value="Selaginella moellendorffii">Selaginella moellendorffii</option> - <option value="Setaria italica">Setaria italica</option> - <option value="Solanum lycopersicum">Solanum lycopersicum</option> - <option value="Solanum tuberosum">Solanum tuberosum</option> - <option value="Sorghum bicolor">Sorghum bicolor</option> - <option value="Vitis vinifera">Vitis vinifera</option> - <option value="Zea mays">Zea mays</option> + <option value="Populus trichocarpa (Western balsam poplar)">Populus trichocarpa (Western balsam poplar)</option> + <option value="Prunus persica (Peach)">Prunus persica (Peach)</option> + <option value="Selaginella moellendorffii (Spike moss)">Selaginella moellendorffii (Spike moss)</option> + <option value="Setaria italica (Foxtail millet)">Setaria italica (Foxtail millet)</option> + <option value="Solanum lycopersicum (Tomato)">Solanum lycopersicum (Tomato)</option> + <option value="Solanum tuberosum (Potato)">Solanum tuberosum (Potato)</option> + <option value="Sorghum bicolor (Sorghum)">Sorghum bicolor (Sorghum)</option> + <option value="Theobroma cacao (Cocoa)">Theobroma cacao (Cocoa)</option> + <option value="Triticum aestivum (Bread wheat)">Triticum aestivum (Bread wheat)</option> + <option value="Triticum urartu (Einkorn)">Triticum urartu (Einkorn)</option> + <option value="Vitis vinifera (Wine grape)">Vitis vinifera (Wine grape)</option> + <option value="Zea mays (Maize)">Zea mays (Maize)</option> </param> </when> <when value="Metazoa"> <param name="species" type="select" label="The species to use for the gene annotation" help=""> <option value="Acyrthosiphon pisum">Acyrthosiphon pisum</option> - <option value="Aedes aegypti">Aedes aegypti</option> + <option value="Aedes aegypti (Yellow fever mosquito)">Aedes aegypti (Yellow fever mosquito)</option> <option value="Amphimedon queenslandica">Amphimedon queenslandica</option> <option value="Anopheles darlingi">Anopheles darlingi</option> - <option value="Anopheles gambiae">Anopheles gambiae</option> - <option value="Apis mellifera">Apis mellifera</option> - <option value="Atta cephalotes">Atta cephalotes</option> - <option value="Bombyx mori">Bombyx mori</option> - <option value="Brugia malayi">Brugia malayi</option> - <option value="Caenorhabditis brenneri">Caenorhabditis brenneri</option> - <option value="Caenorhabditis briggsae">Caenorhabditis briggsae</option> - <option value="Caenorhabditis elegans">Caenorhabditis elegans</option> - <option value="Caenorhabditis japonica">Caenorhabditis japonica</option> - <option value="Caenorhabditis remanei">Caenorhabditis remanei</option> - <option value="Culex quinquefasciatus">Culex quinquefasciatus</option> - <option value="Danaus plexippus">Danaus plexippus</option> - <option value="Daphnia pulex">Daphnia pulex</option> - <option value="Drosophila ananassae">Drosophila ananassae</option> - <option value="Drosophila erecta">Drosophila erecta</option> - <option value="Drosophila grimshawi">Drosophila grimshawi</option> - <option value="Drosophila melanogaster">Drosophila melanogaster</option> - <option value="Drosophila mojavensis">Drosophila mojavensis</option> - <option value="Drosophila persimilis">Drosophila persimilis</option> - <option value="Drosophila pseudoobscura">Drosophila pseudoobscura</option> - <option value="Drosophila sechellia">Drosophila sechellia</option> - <option value="Drosophila simulans">Drosophila simulans</option> - <option value="Drosophila virilis">Drosophila virilis</option> - <option value="Drosophila willistoni">Drosophila willistoni</option> - <option value="Drosophila yakuba">Drosophila yakuba</option> - <option value="Heliconius melpomene">Heliconius melpomene</option> - <option value="Ixodes scapularis">Ixodes scapularis</option> - <option value="Loa loa">Loa loa</option> - <option value="Megaselia scalaris">Megaselia scalaris</option> - <option value="Nasonia vitripennis">Nasonia vitripennis</option> - <option value="Nematostella vectensis">Nematostella vectensis</option> - <option value="Pediculus humanus">Pediculus humanus</option> - <option value="Pristionchus pacificus">Pristionchus pacificus</option> - <option value="Schistosoma mansoni">Schistosoma mansoni</option> - <option value="Strigamia maritima">Strigamia maritima</option> - <option value="Strongylocentrotus purpuratus">Strongylocentrotus purpuratus</option> - <option value="Tribolium castaneum">Tribolium castaneum</option> - <option value="Trichinella spiralis">Trichinella spiralis</option> - <option value="Trichoplax adhaerens">Trichoplax adhaerens</option> + <option value="Anopheles gambiae (African malaria mosquito) ">Anopheles gambiae (African malaria mosquito) </option> + <option value="Apis mellifera ">Apis mellifera </option> + <option value="Atta cephalotes ">Atta cephalotes </option> + <option value="Bombyx mori ">Bombyx mori </option> + <option value="Brugia malayi ">Brugia malayi </option> + <option value="Caenorhabditis brenneri ">Caenorhabditis brenneri </option> + <option value="Caenorhabditis briggsae ">Caenorhabditis briggsae </option> + <option value="Caenorhabditis elegans ">Caenorhabditis elegans </option> + <option value="Caenorhabditis japonica ">Caenorhabditis japonica </option> + <option value="Caenorhabditis remanei ">Caenorhabditis remanei </option> + <option value="Culex quinquefasciatus (Southern house mosquito) ">Culex quinquefasciatus (Southern house mosquito) </option> + <option value="Danaus plexippus ">Danaus plexippus </option> + <option value="Daphnia pulex ">Daphnia pulex </option> + <option value="Dendroctonus ponderosae">Dendroctonus ponderosae</option> + <option value="Drosophila ananassae ">Drosophila ananassae </option> + <option value="Drosophila erecta ">Drosophila erecta </option> + <option value="Drosophila grimshawi ">Drosophila grimshawi </option> + <option value="Drosophila melanogaster (Fruit fly) ">Drosophila melanogaster (Fruit fly) </option> + <option value="Drosophila mojavensis ">Drosophila mojavensis </option> + <option value="Drosophila persimilis ">Drosophila persimilis </option> + <option value="Drosophila pseudoobscura ">Drosophila pseudoobscura </option> + <option value="Drosophila sechellia ">Drosophila sechellia </option> + <option value="Drosophila simulans ">Drosophila simulans </option> + <option value="Drosophila virilis ">Drosophila virilis </option> + <option value="Drosophila willistoni ">Drosophila willistoni </option> + <option value="Drosophila yakuba ">Drosophila yakuba </option> + <option value="Heliconius melpomene ">Heliconius melpomene </option> + <option value="Helobdella robusta">Helobdella robusta</option> + <option value="Ixodes scapularis (Black-legged tick) ">Ixodes scapularis (Black-legged tick) </option> + <option value="Loa loa ">Loa loa </option> + <option value="Lottia gigantea">Lottia gigantea</option> + <option value="Megaselia scalaris ">Megaselia scalaris </option> + <option value="Melitaea cinxia">Melitaea cinxia</option> + <option value="Mnemiopsis leidyi">Mnemiopsis leidyi</option> + <option value="Nasonia vitripennis ">Nasonia vitripennis </option> + <option value="Nematostella vectensis ">Nematostella vectensis </option> + <option value="Onchocerca volvulus">Onchocerca volvulus</option> + <option value="Pediculus humanus (Human louse) ">Pediculus humanus (Human louse) </option> + <option value="Pristionchus pacificus ">Pristionchus pacificus </option> + <option value="Rhodnius prolixus">Rhodnius prolixus</option> + <option value="Schistosoma mansoni ">Schistosoma mansoni </option> + <option value="Solenopsis invicta (Red fire ant)">Solenopsis invicta (Red fire ant)</option> + <option value="Strigamia maritima ">Strigamia maritima </option> + <option value="Strongylocentrotus purpuratus ">Strongylocentrotus purpuratus </option> + <option value="Tetranychus urticae">Tetranychus urticae</option> + <option value="Tribolium castaneum (red flour beetle) ">Tribolium castaneum (red flour beetle) </option> + <option value="Trichinella spiralis ">Trichinella spiralis </option> + <option value="Trichoplax adhaerens ">Trichoplax adhaerens </option> + <option value="Zootermopsis nevadensis">Zootermopsis nevadensis</option> </param> </when> <when value="Fungi"> @@ -281,27 +326,38 @@ <option value="Aspergillus niger">Aspergillus niger</option> <option value="Aspergillus oryzae">Aspergillus oryzae</option> <option value="Aspergillus terreus">Aspergillus terreus</option> - <option value="Botryotinia fuckeliana">Botryotinia fuckeliana</option> + <option value="Blumeria graminis">Blumeria graminis</option> + <option value="Botrytis cinerea">Botrytis cinerea</option> + <option value="Colletotrichum gloeosporioides">Colletotrichum gloeosporioides</option> + <option value="Colletotrichum higginsianum">Colletotrichum higginsianum</option> + <option value="Colletotrichum orbiculare">Colletotrichum orbiculare</option> <option value="Cryptococcus neoformans">Cryptococcus neoformans</option> + <option value="Dothistroma septosporum">Dothistroma septosporum</option> + <option value="Fusarium fujikuroi">Fusarium fujikuroi</option> + <option value="Fusarium graminearum">Fusarium graminearum</option> <option value="Fusarium oxysporum">Fusarium oxysporum</option> + <option value="Fusarium pseudograminearum">Fusarium pseudograminearum</option> + <option value="Fusarium solani">Fusarium solani</option> + <option value="Fusarium verticillioides">Fusarium verticillioides</option> <option value="Gaeumannomyces graminis">Gaeumannomyces graminis</option> - <option value="Gibberella moniliformis">Gibberella moniliformis</option> - <option value="Gibberella zeae">Gibberella zeae</option> - <option value="Glomerella graminicola">Glomerella graminicola</option> + <option value="Colletotrichum graminicola">Colletotrichum graminicola</option> <option value="Komagataella pastoris">Komagataella pastoris</option> <option value="Leptosphaeria maculans">Leptosphaeria maculans</option> <option value="Magnaporthe oryzae">Magnaporthe oryzae</option> <option value="Magnaporthe poae">Magnaporthe poae</option> <option value="Melampsora larici-populina">Melampsora larici-populina</option> - <option value="Nectria haematococca">Nectria haematococca</option> <option value="Neosartorya fischeri">Neosartorya fischeri</option> <option value="Neurospora crassa">Neurospora crassa</option> <option value="Phaeosphaeria nodorum">Phaeosphaeria nodorum</option> <option value="Puccinia graminis">Puccinia graminis</option> + <option value="Puccinia graminis Ug99">Puccinia graminis Ug99</option> <option value="Puccinia triticina">Puccinia triticina</option> <option value="Pyrenophora teres">Pyrenophora teres</option> <option value="Pyrenophora tritici-repentis">Pyrenophora tritici-repentis</option> <option value="Saccharomyces cerevisiae">Saccharomyces cerevisiae</option> + <option value="Schizosaccharomyces cryophilus">Schizosaccharomyces cryophilus</option> + <option value="Schizosaccharomyces japonicus">Schizosaccharomyces japonicus</option> + <option value="Schizosaccharomyces octosporus">Schizosaccharomyces octosporus</option> <option value="Schizosaccharomyces pombe">Schizosaccharomyces pombe</option> <option value="Sclerotinia sclerotiorum">Sclerotinia sclerotiorum</option> <option value="Sporisorium reilianum">Sporisorium reilianum</option> @@ -309,6 +365,8 @@ <option value="Trichoderma virens">Trichoderma virens</option> <option value="Tuber melanosporum">Tuber melanosporum</option> <option value="Ustilago maydis">Ustilago maydis</option> + <option value="Verticillium dahliae JR2">Verticillium dahliae JR2</option> + <option value="Verticillium dahliae">Verticillium dahliae</option> <option value="Yarrowia lipolytica">Yarrowia lipolytica</option> <option value="Zymoseptoria tritici">Zymoseptoria tritici</option> </param> @@ -316,70 +374,77 @@ <when value="Vertebrates"> <param name="species" type="select" label="The species to use for the gene annotation" help=""> - <option value="Ailuropoda melanoleuca">Ailuropoda melanoleuca</option> - <option value="Anolis carolinensis">Anolis carolinensis</option> - <option value="Bos taurus">Bos taurus</option> - <option value="Caenorhabditis elegans">Caenorhabditis elegans</option> - <option value="Callithrix jacchus">Callithrix jacchus</option> - <option value="Canis familiaris">Canis familiaris</option> - <option value="Cavia porcellus">Cavia porcellus</option> - <option value="Choloepus hoffmanni">Choloepus hoffmanni</option> - <option value="Ciona intestinalis">Ciona intestinalis</option> - <option value="Ciona savignyi">Ciona savignyi</option> - <option value="Danio rerio">Danio rerio</option> - <option value="Dasypus novemcinctus">Dasypus novemcinctus</option> - <option value="Dipodomys ordii">Dipodomys ordii</option> - <option value="Drosophila melanogaster">Drosophila melanogaster</option> - <option value="Echinops telfairi">Echinops telfairi</option> - <option value="Equus caballus">Equus caballus</option> - <option value="Erinaceus europaeus">Erinaceus europaeus</option> - <option value="Felis catus">Felis catus</option> - <option value="Gallus gallus">Gallus gallus</option> - <option value="Gasterosteus aculeatus">Gasterosteus aculeatus</option> - <option value="Gorilla gorilla">Gorilla gorilla</option> - <option value="Homo sapiens">Homo sapiens</option> - <option value="Ictidomys tridecemlineatus">Ictidomys tridecemlineatus</option> - <option value="Latimeria chalumnae">Latimeria chalumnae</option> - <option value="Loxodonta africana">Loxodonta africana</option> - <option value="Macaca mulatta">Macaca mulatta</option> - <option value="Macropus eugenii">Macropus eugenii</option> - <option value="Meleagris gallopavo">Meleagris gallopavo</option> - <option value="Microcebus murinus">Microcebus murinus</option> - <option value="Monodelphis domestica">Monodelphis domestica</option> - <option value="Mus musculus">Mus musculus</option> - <option value="Mustela putorius furo">Mustela putorius furo</option> - <option value="Myotis lucifugus">Myotis lucifugus</option> - <option value="Nomascus leucogenys">Nomascus leucogenys</option> - <option value="Ochotona princeps">Ochotona princeps</option> - <option value="Oreochromis niloticus">Oreochromis niloticus</option> - <option value="Ornithorhynchus anatinus">Ornithorhynchus anatinus</option> - <option value="Oryctolagus cuniculus">Oryctolagus cuniculus</option> - <option value="Oryzias latipes">Oryzias latipes</option> - <option value="Otolemur garnettii">Otolemur garnettii</option> - <option value="Pan troglodytes">Pan troglodytes</option> - <option value="Petromyzon marinus">Petromyzon marinus</option> - <option value="Pelodiscus sinensis">Pelodiscus sinensis</option> - <option value="Pongo abelii">Pongo abelii</option> - <option value="Procavia capensis">Procavia capensis</option> - <option value="Pteropus vampyrus">Pteropus vampyrus</option> - <option value="Rattus norvegicus">Rattus norvegicus</option> - <option value="Saccharomyces cerevisiae">Saccharomyces cerevisiae</option> - <option value="Sarcophilus harrisii">Sarcophilus harrisii</option> - <option value="Sorex araneus">Sorex araneus</option> - <option value="Sus scrofa">Sus scrofa</option> - <option value="Taeniopygia guttata">Taeniopygia guttata</option> - <option value="Takifugu rubripes">Takifugu rubripes</option> - <option value="Tarsius syrichta">Tarsius syrichta</option> - <option value="Tetraodon nigroviridis">Tetraodon nigroviridis</option> - <option value="Tupaia belangeri">Tupaia belangeri</option> - <option value="Tursiops truncatus">Tursiops truncatus</option> - <option value="Vicugna pacos">Vicugna pacos</option> - <option value="Xenopus tropicalis">Xenopus tropicalis</option> - <option value="Xiphophorus maculatus">Xiphophorus maculatus</option> + <option value="Alpaca (Vicugna pacos)">Alpaca (Vicugna pacos)</option> + <option value="Amazon molly (Poecilia formosa)">Amazon molly (Poecilia formosa)</option> + <option value="Anole lizard (Anolis carolinensis)">Anole lizard (Anolis carolinensis)</option> + <option value="Armadillo (Dasypus novemcinctus)">Armadillo (Dasypus novemcinctus)</option> + <option value="Bushbaby (Otolemur garnettii)">Bushbaby (Otolemur garnettii)</option> + <option value="C. elegans (Caenorhabditis elegans)">C. elegans (Caenorhabditis elegans)</option> + <option value="C.intestinalis (Ciona intestinalis)">C.intestinalis (Ciona intestinalis)</option> + <option value="C.savignyi (Ciona savignyi)">C.savignyi (Ciona savignyi)</option> + <option value="Cat (Felis catus)">Cat (Felis catus)</option> + <option value="Cave fish (Astyanax mexicanus)">Cave fish (Astyanax mexicanus)</option> + <option value="Chicken (Gallus gallus)">Chicken (Gallus gallus)</option> + <option value="Chimpanzee (Pan troglodytes)">Chimpanzee (Pan troglodytes)</option> + <option value="Chinese softshell turtle (Pelodiscus sinensis)">Chinese softshell turtle (Pelodiscus sinensis)</option> + <option value="Cod (Gadus morhua)">Cod (Gadus morhua)</option> + <option value="Coelacanth (Latimeria chalumnae)">Coelacanth (Latimeria chalumnae)</option> + <option value="Cow (Bos taurus)">Cow (Bos taurus)</option> + <option value="Dog (Canis lupus familiaris)">Dog (Canis lupus familiaris)</option> + <option value="Dolphin (Tursiops truncatus)">Dolphin (Tursiops truncatus)</option> + <option value="Duck (Anas platyrhynchos)">Duck (Anas platyrhynchos)</option> + <option value="Elephant (Loxodonta africana)">Elephant (Loxodonta africana)</option> + <option value="Ferret (Mustela putorius furo)">Ferret (Mustela putorius furo)</option> + <option value="Flycatcher (Ficedula albicollis)">Flycatcher (Ficedula albicollis)</option> + <option value="Fruitfly (Drosophila melanogaster)">Fruitfly (Drosophila melanogaster)</option> + <option value="Fugu (Takifugu rubripes)">Fugu (Takifugu rubripes)</option> + <option value="Gibbon (Nomascus leucogenys)">Gibbon (Nomascus leucogenys)</option> + <option value="Gorilla (Gorilla gorilla gorilla)">Gorilla (Gorilla gorilla gorilla)</option> + <option value="Guinea Pig (Cavia porcellus)">Guinea Pig (Cavia porcellus)</option> + <option value="Hedgehog (Erinaceus europaeus)">Hedgehog (Erinaceus europaeus)</option> + <option value="Horse (Equus caballus)">Horse (Equus caballus)</option> + <option value="Human (Homo sapiens)">Human (Homo sapiens)</option> + <option value="Hyrax (Procavia capensis)">Hyrax (Procavia capensis)</option> + <option value="Kangaroo rat (Dipodomys ordii)">Kangaroo rat (Dipodomys ordii)</option> + <option value="Lamprey (Petromyzon marinus)">Lamprey (Petromyzon marinus)</option> + <option value="Lesser hedgehog tenrec (Echinops telfairi)">Lesser hedgehog tenrec (Echinops telfairi)</option> + <option value="Macaque (Macaca mulatta)">Macaque (Macaca mulatta)</option> + <option value="Marmoset (Callithrix jacchus)">Marmoset (Callithrix jacchus)</option> + <option value="Medaka (Oryzias latipes)">Medaka (Oryzias latipes)</option> + <option value="Megabat (Pteropus vampyrus)">Megabat (Pteropus vampyrus)</option> + <option value="Microbat (Myotis lucifugus)">Microbat (Myotis lucifugus)</option> + <option value="Mouse (Mus musculus)">Mouse (Mus musculus)</option> + <option value="Mouse Lemur (Microcebus murinus)">Mouse Lemur (Microcebus murinus)</option> + <option value="Opossum (Monodelphis domestica)">Opossum (Monodelphis domestica)</option> + <option value="Orangutan (Pongo abelii)">Orangutan (Pongo abelii)</option> + <option value="Panda (Ailuropoda melanoleuca)">Panda (Ailuropoda melanoleuca)</option> + <option value="Pig (Sus scrofa)">Pig (Sus scrofa)</option> + <option value="Pika (Ochotona princeps)">Pika (Ochotona princeps)</option> + <option value="Platyfish (Xiphophorus maculatus)">Platyfish (Xiphophorus maculatus)</option> + <option value="Platypus (Ornithorhynchus anatinus)">Platypus (Ornithorhynchus anatinus)</option> + <option value="Rabbit (Oryctolagus cuniculus)">Rabbit (Oryctolagus cuniculus)</option> + <option value="Rat (Rattus norvegicus)">Rat (Rattus norvegicus)</option> + <option value="S. cerevisiae (Saccharomyces cerevisiae)">S. cerevisiae (Saccharomyces cerevisiae)</option> + <option value="Sheep (Ovis aries)">Sheep (Ovis aries)</option> + <option value="Shrew (Sorex araneus)">Shrew (Sorex araneus)</option> + <option value="Sloth (Choloepus hoffmanni)">Sloth (Choloepus hoffmanni)</option> + <option value="Spotted gar (Lepisosteus oculatus)">Spotted gar (Lepisosteus oculatus)</option> + <option value="Squirrel (Ictidomys tridecemlineatus)">Squirrel (Ictidomys tridecemlineatus)</option> + <option value="Stickleback (Gasterosteus aculeatus)">Stickleback (Gasterosteus aculeatus)</option> + <option value="Tarsier (Tarsius syrichta)">Tarsier (Tarsius syrichta)</option> + <option value="Tasmanian devil (Sarcophilus harrisii)">Tasmanian devil (Sarcophilus harrisii)</option> + <option value="Tetraodon (Tetraodon nigroviridis)">Tetraodon (Tetraodon nigroviridis)</option> + <option value="Tilapia (Oreochromis niloticus)">Tilapia (Oreochromis niloticus)</option> + <option value="Tree Shrew (Tupaia belangeri)">Tree Shrew (Tupaia belangeri)</option> + <option value="Turkey (Meleagris gallopavo)">Turkey (Meleagris gallopavo)</option> + <option value="Vervet-AGM (Chlorocebus sabaeus)">Vervet-AGM (Chlorocebus sabaeus)</option> + <option value="Wallaby (Macropus eugenii)">Wallaby (Macropus eugenii)</option> + <option value="Xenopus (Xenopus tropicalis)">Xenopus (Xenopus tropicalis)</option> + <option value="Zebra Finch (Taeniopygia guttata)">Zebra Finch (Taeniopygia guttata)</option> + <option value="Zebrafish (Danio rerio)">Zebrafish (Danio rerio)</option> </param> </when> </conditional> - <conditional name="processing_options"> <param name="processing_options_selector" type="select" label="Specify Advanced PeptideShaker Processing Options"> <option value="no" selected="True">Default Processing Options</option> @@ -390,7 +455,7 @@ <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> - <param name="protein_fraction_mw_confidence" label="Minimum confidence required for a protein in the fraction MW plot" value="" type="float" + <param name="protein_fraction_mw_confidence" value="95.0" type="float" label="Minimum confidence required for a protein in the fraction MW plot" help="default 95%: '95.0'" /> <conditional name="ptm_score"> <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization"> @@ -415,75 +480,107 @@ </param> <when value="no" /> <when value="yes"> - <param name="min_peptide_length" label="Minimum Peptide Length" value="6" type="integer" /> - <param name="max_peptide_length" label="Maximum Peptide Length" value="30" type="integer" /> - <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)" /> + <param name="min_peptide_length" type="integer" label="Minimum Peptide Length" value="6" /> + <param name="max_peptide_length" type="integer" label="Maximum Peptide Length" value="30" /> + <param name="max_precursor_error" type="float" label="Maximum Precursor Error" value="10" + help="Next option specifies units (Da or ppm)" /> <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select"> <option value="0">ppm</option> <option value="1">Daltons</option> </param> - <param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" /> - <param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" /> - <param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" /> + <!--param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" /--> + <!--param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" /--> + <!--param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" /--> <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" /> </when> </conditional> - <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options"> + <option value="zip">Zip File for import to Desktop App</option> <option value="mzidentML" selected="True">mzidentML File</option> - <option value="3" selected="True">Peptide Report</option> - <option value="4" selected="True">Protein Report</option> - <option value="2">PSM Report</option> + <option value="3" >PSM Report</option> + <option value="4" >Peptide Phosphorylation Report</option> + <option value="5" >Peptide Report</option> + <option value="6" >Protein Phosphorylation Report</option> + <option value="7" >Protein Report</option> + <option value="2">PSM Phosphorylation Report</option> <option value="0">Certificate of Analysis</option> <option value="1">Hierarchical Report</option> <option value="cps">CPS file</option> <validator type="no_options" message="Please select at least one output file" /> </param> + </inputs> <outputs> <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file"> <filter>'mzidentML' in outputs</filter> </data> - <data format="cps" name="output" from_work_dir="peptide_shaker_output.cps" label="${tool.name} on ${on_string}: CPS file"> + <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cps" label="${tool.name} on ${on_string}: CPS file"> <filter>'cps' in outputs</filter> </data> + <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive"> + <filter>'zip' in outputs</filter> + </data> <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters"> <filter>'0' in outputs</filter> </data> - <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report"> - <filter>'2' in outputs</filter> - </data> - <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report"> - <filter>'3' in outputs</filter> - </data> - <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report"> - <filter>'4' in outputs</filter> - </data> <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report"> <filter>'1' in outputs</filter> </data> + <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report"> + <filter>'2' in outputs</filter> + </data> + <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report"> + <filter>'3' in outputs</filter> + </data> + <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report"> + <filter>'4' in outputs</filter> + </data> + <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report"> + <filter>'5' in outputs</filter> + </data> + <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report"> + <filter>'6' in outputs</filter> + </data> + <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report"> + <filter>'7' in outputs</filter> + </data> </outputs> <tests> <test> - <param name="input_database" value="tinydb.fasta"/> - <param name="peak_lists" value="tinyspectra.mgf"/> - <param name="precursor_ion_tol" value="100"/> - <param name="fixed_modifications" value="carbamidomethyl c"/> - <param name="variable_modifications" value="oxidation of m"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="3"/> + <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> <param name="species_type_selector" value="no_species_type"/> <param name="processing_options_selector" value="no"/> <param name="filtering_options_selector" value="no"/> - <!--param name="xtandem_selector" value="no"/>--> - <param name="xtandem_selector" value="yes"/> - <param name="xtandem_selector.xtandem_refine_selector" value="yes"/> - - <param name="omssa_selector" value="no"/> - <param name="msgf_selector" value="yes"/> - <param name="ms_amanda_selector" value="no"/> - - <output name="output" file="tinyoutput.cps" compare="sim_size" delta="600" /> + <param name="outputs" value="zip,cps,3"/> + <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="600" /> + <output name="output_cps" file="peptide_shaker_result1.cps" ftype="peptideshaker_archive" compare="sim_size" delta="600" /> + <output name="output_psm" file="peptide_shaker_psm_result1.tabular" ftype="tabular" /> + </test> + <test> + <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> + <param name="species_type_selector" value="no_species_type"/> + <param name="processing_options_selector" value="no"/> + <param name="filtering_options_selector" value="yes"/> + <param name="min_peptide_length" value="1"/> + <param name="outputs" value="0,1,2,3,4,5,6,7"/> + <output name="output_certificate" file="peptide_shaker_certificate_result2.tabular" ftype="tabular" lines_diff="4"/> + <output name="output_hierarchical" file="peptide_shaker_hierarchical_result2.tabular" ftype="tabular" /> + <output name="output_psm" file="peptide_shaker_psm_result2.tabular" ftype="tabular" /> + <output name="output_psm_phosphorylation" file="peptide_shaker_psm_phoshorylation_result2.tabular" ftype="tabular" /> + <output name="output_peptides" file="peptide_shaker_peptides_result2.tabular" ftype="tabular" /> + <output name="output_peptides_phosphorylation" file="peptide_shaker_peptides_phoshorylation_result2.tabular" ftype="tabular" /> + <output name="output_proteins" file="peptide_shaker_proteins_result2.tabular" ftype="tabular" /> + <output name="output_proteins_phosphorylation" file="peptide_shaker_proteins_phoshorylation_result2.tabular" ftype="tabular" /> + </test> + <test> + <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> + <param name="species_type_selector" value="Vertebrates"/> + <param name="species" value="Human (Homo sapiens)"/> + <param name="processing_options_selector" value="no"/> + <param name="filtering_options_selector" value="yes"/> + <param name="min_peptide_length" value="1"/> + <param name="outputs" value="5"/> + <output name="output_peptides" file="peptide_shaker_peptides_result3.tabular" ftype="tabular" /> </test> </tests> <help> @@ -505,8 +602,8 @@ ---------- * Protein(s): Protein(s) to which the peptide can be attached -* Sequence: Sequence of the peptide -* Variable Modifications: The variable modifications +* Sequence: Sequence of the peptide +* Variable Modifications: The variable modifications * D-score: D-score for variable PTM localization * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization. * Localization Confidence: The confidence in variable PTM localization. @@ -636,8 +733,6 @@ * Validation: Indicates the validation level of the protein group. - - ------ **Citation**
--- a/searchgui.xml Mon Dec 15 21:33:25 2014 -0500 +++ b/searchgui.xml Mon Feb 16 04:18:17 2015 -0500 @@ -1,25 +1,27 @@ -<tool id="search_gui" name="Search GUI" version="1.23.0"> +<tool id="search_gui" name="Search GUI" version="1.24.0"> <description> Perform protein identification using various search engines and prepare results for input to Peptide Shaker </description> <requirements> - <requirement type="package" version="1.23">searchgui</requirement> + <requirement type="package" version="1.24">searchgui</requirement> </requirements> - + <macros> + <import>macros.xml</import> + </macros> <expand macro="stdio" /> <command> <![CDATA[ #from datetime import datetime #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s") #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s") - #set $temp_stderr = 'macs2_stderr' + #set $temp_stderr = "searchgui_stderr" mkdir output; mkdir output_reports; cwd=`pwd`; #for $mgf in $peak_lists: #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf" - ln -s '${mgf}' '${input_name}'; + ln -s -f '${mgf}' '${input_name}'; #end for ##ln -s "${input_database}" input_database.fasta; cp "${input_database}" input_database.fasta; @@ -29,9 +31,9 @@ ########################################### #if $create_decoy: echo "Creating decoy database."; - java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy; - rm input_database.fasta; - cp input_database_concatenated_target_decoy.fasta input_database.fasta; + java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy && + rm input_database.fasta && + cp input_database_concatenated_target_decoy.fasta input_database.fasta && ##ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta; #end if @@ -155,12 +157,19 @@ ## single zip file -output_option 0 + ## mgf and database in output + -output_data 1 + 2>> $temp_stderr) && + (mv output/searchgui_out.zip searchgui_out.zip 2>> $temp_stderr) + + && + exit_code_for_galaxy=\$?; - cat $temp_stderr 2>&1; + cat $temp_stderr 2>&1; (exit \$exit_code_for_galaxy) ]]> </command> @@ -172,7 +181,7 @@ label="Create a concatenated target/decoy database before running PeptideShaker" help="Selecting this option will help PeptideShaker calculate FDR values" /> - <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)" + <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)" help="Select appropriate MGF dataset(s) from history" /> <expand macro="general_options"/> @@ -207,13 +216,16 @@ </param> <when value="no" /> <when value="yes"> - <param name="xtandem_npeaks" label="X!Tandem: Total Peaks" type="integer" value="50" help="Maximum number of peaks to be used from a spectrum"/> + <param name="xtandem_npeaks" type="integer" value="50" + label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/> <param name="xtandem_min_peaks" type="integer" value="15" label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/> <param name="xtandem_min_frag_mz" type="integer" value="200" label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/> - <param name="xtandem_min_prec_mass" label="X!Tandem: Min Precursor Mass" type="integer" value="200" help="Minimum mass of 1+ mass of parent ion to be considered"/> - <param name="xtandem_noise_suppr" label="X!Tandem: Noise Suppression" type="boolean" checked="true" truevalue="1" falsevalue="0" help="Use noise suppression"/> + <param name="xtandem_min_prec_mass" type="integer" value="200" + label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/> + <param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0" + label="X!Tandem: Noise Suppression" help="Use noise suppression"/> <conditional name="xtandem_refine"><!-- -xtandem_refine --> <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement"> @@ -303,33 +315,28 @@ <when value="yes"> </when> </conditional> - </when> </conditional> - </inputs> <outputs> - <data format="bgzip" name="searchgui_results" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" /> + <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" /> </outputs> <tests> <test> - <param name="input_database" value="tinydb.fasta"/> - <param name="peak_lists" value="tinyspectra.mgf"/> + <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> + <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> <param name="precursor_ion_tol" value="100"/> <param name="fixed_modifications" value="carbamidomethyl c"/> <param name="variable_modifications" value="oxidation of m"/> <param name="min_charge" value="1"/> <param name="max_charge" value="3"/> <param name="advanced_type_selector" value="advanced"/> - <!--param name="xtandem_selector" value="no"/>--> <param name="xtandem_selector" value="yes"/> <param name="xtandem_selector.xtandem_refine_selector" value="yes"/> - <param name="omssa_selector" value="no"/> <param name="msgf_selector" value="yes"/> <param name="ms_amanda_selector" value="no"/> - - <output name="output" file="tinyoutput.cps" compare="sim_size" delta="600" /> + <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="600" /> </test> </tests> <help>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_certificate_result2.tabular Mon Feb 16 04:18:17 2015 -0500 @@ -0,0 +1,68 @@ +Project Details1: PeptideShaker Version: 0.37.4-beta +2: Date: Sun Feb 15 09:12:50 CET 2015 +3: Experiment: Galaxy_Experiment_2015021509121423987968 +4: Sample: Sample_2015021509121423987968 +5: Replicate Number: 1 +6: Identification Algorithms: X!Tandem and MS-GF+ +Database Search Parameters + +1: Precursor Accuracy Unit: ppm +2: Precursor Ion m/z Tolerance: 100.0 +3: Fragment Ion m/z Tolerance: 0.5 +4: Enzyme: Trypsin +5: Number of Missed Cleavages: Not implemented +6: Database: input_database.fasta +7: Forward Ion: b +8: Rewind Ion: y +9: Fixed Modifications: carbamidomethyl c +10: Variable Modifications: oxidation of m, acetylation of protein n-term, pyro-cmc, pyro-glu from n-term e, pyro-glu from n-term q +11: Refinement Variable Modifications: +12: Refinement Fixed Modifications: +Input Filters + +1: Minimal Peptide Length: 1 +2: Maximal Peptide Length: 30 +3: Precursor m/z Tolerance: 10.0 +4: Precursor m/z Tolerance Unit: Yes +5: Unrecognized Modifications Discarded: No +Validation Summary + +1: #Validated Proteins: 0.0 +2: Protein Total: 0.0 +3Protein FDR Limit: 1.0 % +4: Protein FNR Limit: 0.0 % +5: Protein Confidence Limit: -1.0 % +6: Protein PEP Limit: 101.0 % +7: Protein Confidence Accuracy: 0.0 % +8: #Validated Peptides: 0.0 +9: Peptide Total: 0.0 +10: Peptide FDR Limit: 1.0 % +11: Peptide FNR Limit: 0.0 % +12: Peptide Confidence Limit: -1.0 % +13: Peptide PEP Limit: 101.0 % +14: Peptide Confidence Accuracy: 0.0 % +15: #Validated PSM: 0.0 +16: PSM Total: 0.0 +17: PSM FDR Limit: 1.0 % +18: PSM FNR Limit: 0.0 % +19: PSM Confidence Limit: -1.0 % +20: PSM PEP Limit: 101.0 % +21: PSM Confidence Accuracy: 0.0 % +Postranslational Modification Scoring Settings + +1: A-score: No +2: Accounting for Neutral Losses: No +3: False Location Rate: 1.0 +Spectrum Counting Parameters + +1: Method: NSAF +2: Validated Matches Only: Yes +Annotation Settings + +1: Intensity Limit: 0.75 +2: Automatic Annotation: Yes +3: Selected Ions: b, y +4: Neutral Losses: NH3, H2O +5: Neutral Losses Sequence Dependence: Yes +6: Selected Charges: 1, 2 +7: Fragment Ion m/z Tolerance: 0.5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_hierarchical_result2.tabular Mon Feb 16 04:18:17 2015 -0500 @@ -0,0 +1,78 @@ + Main Accession Description MW [kDa] Coverage [%] Possible Coverage [%] Spectrum Counting NSAF Confidently Localized Modification Sites # Confidently Localized Modification Sites Ambiguously Localized Modification Sites #Ambiguously Localized Modification Sites PI Secondary Accessions Protein Group #Validated Peptides #Peptides #Unique #Validated PSMs #PSMs Confidence Decoy Validation +1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67 69.88215372568374 3757.96 92.52 0.014450915311500504 Related Proteins cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 15 15 15 39 39 100.0 0 Doubtful + Protein(s) Sequence AAs Before AAs After Variable Modifications Fixed Modifications Localization Confidence #Validated PSMs #PSMs Confidence Decoy Validation +1.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR LK; LK IN; IN 2 2 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.1.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR NH2-ISITTYEEEIEDLHATAR-COOH tinyspectra.mgf Cmpd 752, +MSn(697.6842), 76.3 min -1.0 697.68418 3+ 3+ 2090.0167716836995 0 6.659655420038472 0 100.0 Doubtful +1.1.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR NH2-ISITTYEEEIEDLHATAR-COOH tinyspectra.mgf Cmpd 752, MSn(697.6842), 76.3 min -1.0 697.68418 3+ 3+ 2090.0167716836995 0 6.659655420038472 0 100.0 Doubtful +1.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK AK; AK IS; IS 4 4 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.2.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK NH2-NLLLDANKENGELK-COOH tinyspectra.mgf Cmpd 204, +MSn(524.2825), 35.5 min -1.0 524.28252 3+ 3+ 1569.8362346836998 0 -6.678342042310128 0 100.0 Doubtful +1.2.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK NH2-NLLLDANKENGELK-COOH tinyspectra.mgf Cmpd 207, +MSn(785.9179), 35.7 min -1.0 785.91791 2+ 2+ 1569.8362346836998 0 -9.522288910374096 0 100.0 Doubtful +1.2.3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK NH2-NLLLDANKENGELK-COOH tinyspectra.mgf Cmpd 207, MSn(785.9179), 35.7 min -1.0 785.91791 2+ 2+ 1569.8362346836998 0 -9.522288910374096 0 100.0 Doubtful +1.2.4 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK NH2-NLLLDANKENGELK-COOH tinyspectra.mgf Cmpd 204, MSn(524.2825), 35.5 min -1.0 524.28252 3+ 3+ 1569.8362346836998 0 -6.678342042310128 0 100.0 Doubtful +1.3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR VR; VR LK; LK 2 2 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.3.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR NH2-SLQAENEQLR-COOH tinyspectra.mgf Cmpd 39, +MSn(594.3056), 25.0 min -1.0 594.30561 2+ 2+ 1186.5942146837 0 2.0632379154490605 0 100.0 Doubtful +1.3.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR NH2-SLQAENEQLR-COOH tinyspectra.mgf Cmpd 39, MSn(594.3056), 25.0 min -1.0 594.30561 2+ 2+ 1186.5942146837 0 2.0632379154490605 0 100.0 Doubtful +1.4 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK AR; AR LI; LI 2 2 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.4.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK NH2-INEDRIDELQDKVNK-COOH tinyspectra.mgf Cmpd 81, +MSn(610.3171), 27.0 min -1.0 610.31708 3+ 3+ 1827.9326546837003 0 -1.7717994436305495 0 100.0 Doubtful +1.4.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK NH2-INEDRIDELQDKVNK-COOH tinyspectra.mgf Cmpd 81, MSn(610.3171), 27.0 min -1.0 610.31708 3+ 3+ 1827.9326546837003 0 -1.7717994436305495 0 100.0 Doubtful +1.5 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR MK; MK SN; SN 2 2 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.5.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR NH2-MEIITITNQLQR-COOH tinyspectra.mgf Cmpd 636, +MSn(730.3981), 66.9 min -1.0 730.39814 2+ 2+ 1458.7864506836997 0 -3.233580283650776 0 100.0 Doubtful +1.5.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR NH2-MEIITITNQLQR-COOH tinyspectra.mgf Cmpd 636, MSn(730.3981), 66.9 min -1.0 730.39814 2+ 2+ 1458.7864506836997 0 -3.233580283650776 0 100.0 Doubtful +1.6 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK NK; NK LS; LS 3 3 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.6.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK NH2-LHVEMESMIEELQMLMDAK-COOH tinyspectra.mgf Cmpd 1198, +MSn(1139.0413), 115.6 min -1.0 1139.04127 2+ 2+ 2276.0560846836997 0 5.224764535153943 0 100.0 Doubtful +1.6.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK NH2-LHVEMESMIEELQMLMDAK-COOH tinyspectra.mgf Cmpd 1197, +MSn(759.6966), 115.6 min -1.0 759.69661 3+ 3+ 2276.0560846836997 0 5.228393373659577 0 100.0 Doubtful +1.6.3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK NH2-LHVEMESMIEELQMLMDAK-COOH tinyspectra.mgf Cmpd 1197, MSn(759.6966), 115.6 min -1.0 759.69661 3+ 3+ 2276.0560846836997 0 5.228393373659577 0 100.0 Doubtful +1.7 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR AR; AR QS; QS 2 2 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.7.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR NH2-YESQLSQIR-COOH tinyspectra.mgf Cmpd 67, +MSn(562.2947), 26.3 min -1.0 562.29468 2+ 2+ 1122.5669286837 0 7.00561302556395 0 100.0 Doubtful +1.7.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR NH2-YESQLSQIR-COOH tinyspectra.mgf Cmpd 67, MSn(562.2947), 26.3 min -1.0 562.29468 2+ 2+ 1122.5669286837 0 7.00561302556395 0 100.0 Doubtful +1.8 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR QK; QK SV; SV 4 4 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.8.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR NH2-VGNLEEELEFLR-COOH tinyspectra.mgf Cmpd 875, +MSn(483.2538), 89.2 min -1.0 483.25374 3+ 3+ 1446.7354586837 0 2.7121200881231644 0 100.0 Doubtful +1.8.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR NH2-VGNLEEELEFLR-COOH tinyspectra.mgf Cmpd 871, +MSn(724.3762), 88.9 min -1.0 724.37624 2+ 2+ 1446.7354586837 0 1.7038016610019715 0 100.0 Doubtful +1.8.3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR NH2-VGNLEEELEFLR-COOH tinyspectra.mgf Cmpd 875, MSn(483.2538), 89.2 min -1.0 483.25374 3+ 3+ 1446.7354586837 0 2.7121200881231644 0 100.0 Doubtful +1.8.4 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR NH2-VGNLEEELEFLR-COOH tinyspectra.mgf Cmpd 871, MSn(724.3762), 88.9 min -1.0 724.37624 2+ 2+ 1446.7354586837 0 1.7038016610019715 0 100.0 Doubtful +1.9 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR RR; RR AS; AS 2 2 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.9.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH tinyspectra.mgf Cmpd 220, +MSn(824.3852), 36.3 min -1.0 824.38516 3+ 3+ 2470.1263816837 0 2.9391347559636922 0 100.0 Doubtful +1.9.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH tinyspectra.mgf Cmpd 220, MSn(824.3852), 36.3 min -1.0 824.38516 3+ 3+ 2470.1263816837 0 2.9391347559636922 0 100.0 Doubtful +1.10 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR NR; NR SE; SE 4 4 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.10.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR NH2-ISTGYITENIGGFR-COOH tinyspectra.mgf Cmpd 591, +MSn(509.9328), 63.7 min -1.0 509.93283 3+ 3+ 1526.7728996836997 0 2.458444778796749 0 100.0 Doubtful +1.10.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR NH2-ISTGYITENIGGFR-COOH tinyspectra.mgf Cmpd 588, +MSn(764.3961), 63.5 min -1.0 764.39611 2+ 2+ 1526.7728996836997 0 3.1184077735785474 0 100.0 Doubtful +1.10.3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR NH2-ISTGYITENIGGFR-COOH tinyspectra.mgf Cmpd 591, MSn(509.9328), 63.7 min -1.0 509.93283 3+ 3+ 1526.7728996836997 0 2.458444778796749 0 100.0 Doubtful +1.10.4 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR NH2-ISTGYITENIGGFR-COOH tinyspectra.mgf Cmpd 588, MSn(764.3961), 63.5 min -1.0 764.39611 2+ 2+ 1526.7728996836997 0 3.1184077735785474 0 100.0 Doubtful +1.11 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK RR; RR NL; NL 2 2 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.11.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK NH2-EFDVEPLKEAYQAEIDEAK-COOH tinyspectra.mgf Cmpd 736, +MSn(742.0258), 75.1 min -1.0 742.02585 3+ 3+ 2223.0583016837 0 -1.1594749443833878 0 100.0 Doubtful +1.11.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK NH2-EFDVEPLKEAYQAEIDEAK-COOH tinyspectra.mgf Cmpd 736, MSn(742.0258), 75.1 min -1.0 742.02585 3+ 3+ 2223.0583016837 0 -1.1594749443833878 0 100.0 Doubtful +1.12 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK GR; GR DM; DM 2 2 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.12.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK NH2-ASLGMAAGVAGGIATK-COOH tinyspectra.mgf Cmpd 357, +MSn(687.8723), 46.6 min -1.0 687.87224 2+ 2+ 1373.7336876837 0 -2.733506911277659 0 100.0 Doubtful +1.12.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK NH2-ASLGMAAGVAGGIATK-COOH tinyspectra.mgf Cmpd 357, MSn(687.8723), 46.6 min -1.0 687.87224 2+ 2+ 1373.7336876837 0 -2.733506911277659 0 100.0 Doubtful +1.13 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR AK; AK; AK NS; NS; NS 2 2 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.13.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR NH2-KGDIIATVDEWGPVNR-COOH tinyspectra.mgf Cmpd 582, +MSn(590.6452), 63.2 min -1.0 590.64518 3+ 3+ 1768.9107986836998 0 1.6433558579610066 0 100.0 Doubtful +1.13.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR NH2-KGDIIATVDEWGPVNR-COOH tinyspectra.mgf Cmpd 582, MSn(590.6452), 63.2 min -1.0 590.64518 3+ 3+ 1768.9107986836998 0 1.6433558579610066 0 100.0 Doubtful +1.14 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK DR; DR; DR ID; ID; ID 4 4 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.14.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK NH2-LISATSISPEHK-COOH tinyspectra.mgf Cmpd 75, +MSn(641.8547), 26.7 min -1.0 641.85466 2+ 2+ 1281.6928656837001 0 1.4811651380377848 0 100.0 Doubtful +1.14.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK NH2-LISATSISPEHK-COOH tinyspectra.mgf Cmpd 72, +MSn(428.2391), 26.6 min -1.0 428.23909 3+ 3+ 1281.6928656837001 0 2.0042705774391996 0 100.0 Doubtful +1.14.3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK NH2-LISATSISPEHK-COOH tinyspectra.mgf Cmpd 72, MSn(428.2391), 26.6 min -1.0 428.23909 3+ 3+ 1281.6928656837001 0 2.0042705774391996 0 100.0 Doubtful +1.14.4 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK NH2-LISATSISPEHK-COOH tinyspectra.mgf Cmpd 75, MSn(641.8547), 26.7 min -1.0 641.85466 2+ 2+ 1281.6928656837001 0 1.4811651380377848 0 100.0 Doubtful +1.15 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR SK; SK; SK SK; SK; SK 2 2 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1.15.1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR NH2-SVISIGEVESEGQYVTLENTSSGR-COOH tinyspectra.mgf Cmpd 758, +MSn(847.7508), 76.8 min -1.0 847.75082 3+ 3+ 2540.2241966836996 0 2.5298047449054923 0 100.0 Doubtful +1.15.2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR NH2-SVISIGEVESEGQYVTLENTSSGR-COOH tinyspectra.mgf Cmpd 758, MSn(847.7508), 76.8 min -1.0 847.75082 3+ 3+ 2540.2241966836996 0 2.5298047449054923 0 100.0 Doubtful +2 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91 69.9696370486838 325.2 100.0 0.0032520325203252032 Related Proteins cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 1 1 1 2 2 100.0 0 Doubtful + Protein(s) Sequence AAs Before AAs After Variable Modifications Fixed Modifications Localization Confidence #Validated PSMs #PSMs Confidence Decoy Validation +2.1 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91; cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK MR; MR YQ; YQ 2 2 100.0 0 Doubtful + Protein(s) Sequence Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +2.1.1 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK NH2-EIRDEYDNQLNLLSADLESK-COOH tinyspectra.mgf Cmpd 748, +MSn(789.0604), 76.1 min -1.0 789.06034 3+ 3+ 2364.1444886837 0 6.210765906697086 0 100.0 Doubtful +2.1.2 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK NH2-EIRDEYDNQLNLLSADLESK-COOH tinyspectra.mgf Cmpd 748, MSn(789.0604), 76.1 min -1.0 789.06034 3+ 3+ 2364.1444886837 0 6.210765906697086 0 100.0 Doubtful
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_peptides_phoshorylation_result2.tabular Mon Feb 16 04:18:17 2015 -0500 @@ -0,0 +1,17 @@ + Protein(s) Sequence Modified Sequence AAs Before AAs After Variable Modifications Fixed Modifications Localization Confidence Confident Phosphosites #Confident Phosphosites Ambiguous Phosphosites #Ambiguous Phosphosites #Validated PSMs #PSMs Confidence Decoy Validation +1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR NH2-ISITTYEEEIEDLHATAR-COOH LK; LK IN; IN 2 2 100.0 0 Doubtful +2 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91; cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK NH2-EIRDEYDNQLNLLSADLESK-COOH MR; MR YQ; YQ 2 2 100.0 0 Doubtful +3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK NH2-NLLLDANKENGELK-COOH AK; AK IS; IS 4 4 100.0 0 Doubtful +4 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR NH2-SLQAENEQLR-COOH VR; VR LK; LK 2 2 100.0 0 Doubtful +5 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK NH2-INEDRIDELQDKVNK-COOH AR; AR LI; LI 2 2 100.0 0 Doubtful +6 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR NH2-MEIITITNQLQR-COOH MK; MK SN; SN 2 2 100.0 0 Doubtful +7 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK NH2-LHVEMESMIEELQMLMDAK-COOH NK; NK LS; LS 3 3 100.0 0 Doubtful +8 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR NH2-YESQLSQIR-COOH AR; AR QS; QS 2 2 100.0 0 Doubtful +9 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR NH2-VGNLEEELEFLR-COOH QK; QK SV; SV 4 4 100.0 0 Doubtful +10 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR NH2-KGDIIATVDEWGPVNR-COOH AK; AK; AK NS; NS; NS 2 2 100.0 0 Doubtful +11 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK NH2-LISATSISPEHK-COOH DR; DR; DR ID; ID; ID 4 4 100.0 0 Doubtful +12 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH RR; RR AS; AS 2 2 100.0 0 Doubtful +13 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR NH2-ISTGYITENIGGFR-COOH NR; NR SE; SE 4 4 100.0 0 Doubtful +14 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK NH2-EFDVEPLKEAYQAEIDEAK-COOH RR; RR NL; NL 2 2 100.0 0 Doubtful +15 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR NH2-SVISIGEVESEGQYVTLENTSSGR-COOH SK; SK; SK SK; SK; SK 2 2 100.0 0 Doubtful +16 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK NH2-ASLGMAAGVAGGIATK-COOH GR; GR DM; DM 2 2 100.0 0 Doubtful
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_peptides_result2.tabular Mon Feb 16 04:18:17 2015 -0500 @@ -0,0 +1,17 @@ + Protein(s) Sequence Modified Sequence AAs Before AAs After Variable Modifications Fixed Modifications Localization Confidence #Validated PSMs #PSMs Confidence Decoy Validation +1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR NH2-ISITTYEEEIEDLHATAR-COOH LK; LK IN; IN 2 2 100.0 0 Doubtful +2 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91; cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK NH2-EIRDEYDNQLNLLSADLESK-COOH MR; MR YQ; YQ 2 2 100.0 0 Doubtful +3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK NH2-NLLLDANKENGELK-COOH AK; AK IS; IS 4 4 100.0 0 Doubtful +4 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR NH2-SLQAENEQLR-COOH VR; VR LK; LK 2 2 100.0 0 Doubtful +5 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK NH2-INEDRIDELQDKVNK-COOH AR; AR LI; LI 2 2 100.0 0 Doubtful +6 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR NH2-MEIITITNQLQR-COOH MK; MK SN; SN 2 2 100.0 0 Doubtful +7 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK NH2-LHVEMESMIEELQMLMDAK-COOH NK; NK LS; LS 3 3 100.0 0 Doubtful +8 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR NH2-YESQLSQIR-COOH AR; AR QS; QS 2 2 100.0 0 Doubtful +9 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR NH2-VGNLEEELEFLR-COOH QK; QK SV; SV 4 4 100.0 0 Doubtful +10 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR NH2-KGDIIATVDEWGPVNR-COOH AK; AK; AK NS; NS; NS 2 2 100.0 0 Doubtful +11 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK NH2-LISATSISPEHK-COOH DR; DR; DR ID; ID; ID 4 4 100.0 0 Doubtful +12 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH RR; RR AS; AS 2 2 100.0 0 Doubtful +13 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR NH2-ISTGYITENIGGFR-COOH NR; NR SE; SE 4 4 100.0 0 Doubtful +14 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK NH2-EFDVEPLKEAYQAEIDEAK-COOH RR; RR NL; NL 2 2 100.0 0 Doubtful +15 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR NH2-SVISIGEVESEGQYVTLENTSSGR-COOH SK; SK; SK SK; SK; SK 2 2 100.0 0 Doubtful +16 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK NH2-ASLGMAAGVAGGIATK-COOH GR; GR DM; DM 2 2 100.0 0 Doubtful
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_peptides_result3.tabular Mon Feb 16 04:18:17 2015 -0500 @@ -0,0 +1,17 @@ + Protein(s) Sequence Modified Sequence AAs Before AAs After Variable Modifications Fixed Modifications Localization Confidence #Validated PSMs #PSMs Confidence Decoy Validation +1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR NH2-ISITTYEEEIEDLHATAR-COOH LK; LK IN; IN 2 2 100.0 0 Doubtful +2 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91; cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK NH2-EIRDEYDNQLNLLSADLESK-COOH MR; MR YQ; YQ 2 2 100.0 0 Doubtful +3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK NH2-NLLLDANKENGELK-COOH AK; AK IS; IS 4 4 100.0 0 Doubtful +4 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR NH2-SLQAENEQLR-COOH VR; VR LK; LK 2 2 100.0 0 Doubtful +5 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK NH2-INEDRIDELQDKVNK-COOH AR; AR LI; LI 2 2 100.0 0 Doubtful +6 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR NH2-MEIITITNQLQR-COOH MK; MK SN; SN 2 2 100.0 0 Doubtful +7 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK NH2-LHVEMESMIEELQMLMDAK-COOH NK; NK LS; LS 3 3 100.0 0 Doubtful +8 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR NH2-YESQLSQIR-COOH AR; AR QS; QS 2 2 100.0 0 Doubtful +9 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR NH2-VGNLEEELEFLR-COOH QK; QK SV; SV 4 4 100.0 0 Doubtful +10 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR NH2-KGDIIATVDEWGPVNR-COOH AK; AK; AK NS; NS; NS 2 2 100.0 0 Doubtful +11 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK NH2-LISATSISPEHK-COOH DR; DR; DR ID; ID; ID 4 4 100.0 0 Doubtful +12 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH RR; RR AS; AS 2 2 100.0 0 Doubtful +13 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR NH2-ISTGYITENIGGFR-COOH NR; NR SE; SE 4 4 100.0 0 Doubtful +14 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK NH2-EFDVEPLKEAYQAEIDEAK-COOH RR; RR NL; NL 2 2 100.0 0 Doubtful +15 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR NH2-SVISIGEVESEGQYVTLENTSSGR-COOH SK; SK; SK SK; SK; SK 2 2 100.0 0 Doubtful +16 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK NH2-ASLGMAAGVAGGIATK-COOH GR; GR DM; DM 2 2 100.0 0 Doubtful
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_proteins_phoshorylation_result2.tabular Mon Feb 16 04:18:17 2015 -0500 @@ -0,0 +1,3 @@ + Main Accession Description Gene Name Chromosome MW [kDa] Coverage [%] Possible Coverage [%] Spectrum Counting NSAF Confident Phosphosites #Confident Phosphosites Ambiguous Phosphosites #Ambiguous Phosphosites PI Secondary Accessions Protein Group #Validated Peptides #Peptides #Unique #Validated PSMs #PSMs Confidence Decoy Validation +1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67 69.88215372568374 3757.96 92.52 0.014450915311500504 0 0 Related Proteins cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 15 15 15 39 39 100.0 0 Doubtful +2 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91 69.9696370486838 325.2 100.0 0.0032520325203252032 0 0 Related Proteins cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 1 1 1 2 2 100.0 0 Doubtful
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_proteins_result2.tabular Mon Feb 16 04:18:17 2015 -0500 @@ -0,0 +1,3 @@ + Main Accession Description Gene Name Chromosome MW [kDa] Coverage [%] Possible Coverage [%] Spectrum Counting NSAF Confidently Localized Modification Sites # Confidently Localized Modification Sites Ambiguously Localized Modification Sites #Ambiguously Localized Modification Sites PI Secondary Accessions Protein Group #Validated Peptides #Peptides #Unique #Validated PSMs #PSMs Confidence Decoy Validation +1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67 69.88215372568374 3757.96 92.52 0.014450915311500504 Related Proteins cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 15 15 15 39 39 100.0 0 Doubtful +2 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91 69.9696370486838 325.2 100.0 0.0032520325203252032 Related Proteins cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 1 1 1 2 2 100.0 0 Doubtful
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_psm_phoshorylation_result2.tabular Mon Feb 16 04:18:17 2015 -0500 @@ -0,0 +1,42 @@ + Protein(s) Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confident Phosphosites #Confident Phosphosites Ambiguous Phosphosites #Ambiguous Phosphosites Confidence Validation +1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR tinyspectra.mgf Cmpd 752, +MSn(697.6842), 76.3 min -1.0 697.68418 3+ 3+ 2090.0167716836995 0 6.659655420038472 0 100.0 Doubtful +2 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK tinyspectra.mgf Cmpd 748, +MSn(789.0604), 76.1 min -1.0 789.06034 3+ 3+ 2364.1444886837 0 6.210765906697086 0 100.0 Doubtful +3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 204, +MSn(524.2825), 35.5 min -1.0 524.28252 3+ 3+ 1569.8362346836998 0 -6.678342042310128 0 100.0 Doubtful +4 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR tinyspectra.mgf Cmpd 39, +MSn(594.3056), 25.0 min -1.0 594.30561 2+ 2+ 1186.5942146837 0 2.0632379154490605 0 100.0 Doubtful +5 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK tinyspectra.mgf Cmpd 81, +MSn(610.3171), 27.0 min -1.0 610.31708 3+ 3+ 1827.9326546837003 0 -1.7717994436305495 0 100.0 Doubtful +6 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR tinyspectra.mgf Cmpd 636, +MSn(730.3981), 66.9 min -1.0 730.39814 2+ 2+ 1458.7864506836997 0 -3.233580283650776 0 100.0 Doubtful +7 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK tinyspectra.mgf Cmpd 1198, +MSn(1139.0413), 115.6 min -1.0 1139.04127 2+ 2+ 2276.0560846836997 0 5.224764535153943 0 100.0 Doubtful +8 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR tinyspectra.mgf Cmpd 67, +MSn(562.2947), 26.3 min -1.0 562.29468 2+ 2+ 1122.5669286837 0 7.00561302556395 0 100.0 Doubtful +9 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 207, +MSn(785.9179), 35.7 min -1.0 785.91791 2+ 2+ 1569.8362346836998 0 -9.522288910374096 0 100.0 Doubtful +10 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK tinyspectra.mgf Cmpd 1197, +MSn(759.6966), 115.6 min -1.0 759.69661 3+ 3+ 2276.0560846836997 0 5.228393373659577 0 100.0 Doubtful +11 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 875, +MSn(483.2538), 89.2 min -1.0 483.25374 3+ 3+ 1446.7354586837 0 2.7121200881231644 0 100.0 Doubtful +12 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR tinyspectra.mgf Cmpd 582, +MSn(590.6452), 63.2 min -1.0 590.64518 3+ 3+ 1768.9107986836998 0 1.6433558579610066 0 100.0 Doubtful +13 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 75, +MSn(641.8547), 26.7 min -1.0 641.85466 2+ 2+ 1281.6928656837001 0 1.4811651380377848 0 100.0 Doubtful +14 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 871, +MSn(724.3762), 88.9 min -1.0 724.37624 2+ 2+ 1446.7354586837 0 1.7038016610019715 0 100.0 Doubtful +15 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR tinyspectra.mgf Cmpd 220, +MSn(824.3852), 36.3 min -1.0 824.38516 3+ 3+ 2470.1263816837 0 2.9391347559636922 0 100.0 Doubtful +16 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 591, +MSn(509.9328), 63.7 min -1.0 509.93283 3+ 3+ 1526.7728996836997 0 2.458444778796749 0 100.0 Doubtful +17 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK tinyspectra.mgf Cmpd 736, +MSn(742.0258), 75.1 min -1.0 742.02585 3+ 3+ 2223.0583016837 0 -1.1594749443833878 0 100.0 Doubtful +18 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 72, +MSn(428.2391), 26.6 min -1.0 428.23909 3+ 3+ 1281.6928656837001 0 2.0042705774391996 0 100.0 Doubtful +19 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 588, +MSn(764.3961), 63.5 min -1.0 764.39611 2+ 2+ 1526.7728996836997 0 3.1184077735785474 0 100.0 Doubtful +20 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR tinyspectra.mgf Cmpd 758, +MSn(847.7508), 76.8 min -1.0 847.75082 3+ 3+ 2540.2241966836996 0 2.5298047449054923 0 100.0 Doubtful +21 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK tinyspectra.mgf Cmpd 357, +MSn(687.8723), 46.6 min -1.0 687.87224 2+ 2+ 1373.7336876837 0 -2.733506911277659 0 100.0 Doubtful +22 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK tinyspectra.mgf Cmpd 736, MSn(742.0258), 75.1 min -1.0 742.02585 3+ 3+ 2223.0583016837 0 -1.1594749443833878 0 100.0 Doubtful +23 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR tinyspectra.mgf Cmpd 636, MSn(730.3981), 66.9 min -1.0 730.39814 2+ 2+ 1458.7864506836997 0 -3.233580283650776 0 100.0 Doubtful +24 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 591, MSn(509.9328), 63.7 min -1.0 509.93283 3+ 3+ 1526.7728996836997 0 2.458444778796749 0 100.0 Doubtful +25 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR tinyspectra.mgf Cmpd 39, MSn(594.3056), 25.0 min -1.0 594.30561 2+ 2+ 1186.5942146837 0 2.0632379154490605 0 100.0 Doubtful +26 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR tinyspectra.mgf Cmpd 67, MSn(562.2947), 26.3 min -1.0 562.29468 2+ 2+ 1122.5669286837 0 7.00561302556395 0 100.0 Doubtful +27 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR tinyspectra.mgf Cmpd 752, MSn(697.6842), 76.3 min -1.0 697.68418 3+ 3+ 2090.0167716836995 0 6.659655420038472 0 100.0 Doubtful +28 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 207, MSn(785.9179), 35.7 min -1.0 785.91791 2+ 2+ 1569.8362346836998 0 -9.522288910374096 0 100.0 Doubtful +29 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 875, MSn(483.2538), 89.2 min -1.0 483.25374 3+ 3+ 1446.7354586837 0 2.7121200881231644 0 100.0 Doubtful +30 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 72, MSn(428.2391), 26.6 min -1.0 428.23909 3+ 3+ 1281.6928656837001 0 2.0042705774391996 0 100.0 Doubtful +31 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK tinyspectra.mgf Cmpd 81, MSn(610.3171), 27.0 min -1.0 610.31708 3+ 3+ 1827.9326546837003 0 -1.7717994436305495 0 100.0 Doubtful +32 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR tinyspectra.mgf Cmpd 758, MSn(847.7508), 76.8 min -1.0 847.75082 3+ 3+ 2540.2241966836996 0 2.5298047449054923 0 100.0 Doubtful +33 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 588, MSn(764.3961), 63.5 min -1.0 764.39611 2+ 2+ 1526.7728996836997 0 3.1184077735785474 0 100.0 Doubtful +34 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 871, MSn(724.3762), 88.9 min -1.0 724.37624 2+ 2+ 1446.7354586837 0 1.7038016610019715 0 100.0 Doubtful +35 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK tinyspectra.mgf Cmpd 1197, MSn(759.6966), 115.6 min -1.0 759.69661 3+ 3+ 2276.0560846836997 0 5.228393373659577 0 100.0 Doubtful +36 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 204, MSn(524.2825), 35.5 min -1.0 524.28252 3+ 3+ 1569.8362346836998 0 -6.678342042310128 0 100.0 Doubtful +37 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK tinyspectra.mgf Cmpd 748, MSn(789.0604), 76.1 min -1.0 789.06034 3+ 3+ 2364.1444886837 0 6.210765906697086 0 100.0 Doubtful +38 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR tinyspectra.mgf Cmpd 582, MSn(590.6452), 63.2 min -1.0 590.64518 3+ 3+ 1768.9107986836998 0 1.6433558579610066 0 100.0 Doubtful +39 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 75, MSn(641.8547), 26.7 min -1.0 641.85466 2+ 2+ 1281.6928656837001 0 1.4811651380377848 0 100.0 Doubtful +40 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR tinyspectra.mgf Cmpd 220, MSn(824.3852), 36.3 min -1.0 824.38516 3+ 3+ 2470.1263816837 0 2.9391347559636922 0 100.0 Doubtful +41 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK tinyspectra.mgf Cmpd 357, MSn(687.8723), 46.6 min -1.0 687.87224 2+ 2+ 1373.7336876837 0 -2.733506911277659 0 100.0 Doubtful
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_psm_result1.tabular Mon Feb 16 04:18:17 2015 -0500 @@ -0,0 +1,42 @@ + Protein(s) Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR tinyspectra.mgf Cmpd 752, +MSn(697.6842), 76.3 min -1.0 697.68418 3+ 3+ 2090.0167716836995 0 6.659655420038472 0 100.0 Doubtful +2 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK tinyspectra.mgf Cmpd 748, +MSn(789.0604), 76.1 min -1.0 789.06034 3+ 3+ 2364.1444886837 0 6.210765906697086 0 100.0 Doubtful +3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 204, +MSn(524.2825), 35.5 min -1.0 524.28252 3+ 3+ 1569.8362346836998 0 -6.678342042310128 0 100.0 Doubtful +4 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR tinyspectra.mgf Cmpd 39, +MSn(594.3056), 25.0 min -1.0 594.30561 2+ 2+ 1186.5942146837 0 2.0632379154490605 0 100.0 Doubtful +5 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK tinyspectra.mgf Cmpd 81, +MSn(610.3171), 27.0 min -1.0 610.31708 3+ 3+ 1827.9326546837003 0 -1.7717994436305495 0 100.0 Doubtful +6 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR tinyspectra.mgf Cmpd 636, +MSn(730.3981), 66.9 min -1.0 730.39814 2+ 2+ 1458.7864506836997 0 -3.233580283650776 0 100.0 Doubtful +7 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK tinyspectra.mgf Cmpd 1198, +MSn(1139.0413), 115.6 min -1.0 1139.04127 2+ 2+ 2276.0560846836997 0 5.224764535153943 0 100.0 Doubtful +8 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR tinyspectra.mgf Cmpd 67, +MSn(562.2947), 26.3 min -1.0 562.29468 2+ 2+ 1122.5669286837 0 7.00561302556395 0 100.0 Doubtful +9 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 207, +MSn(785.9179), 35.7 min -1.0 785.91791 2+ 2+ 1569.8362346836998 0 -9.522288910374096 0 100.0 Doubtful +10 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK tinyspectra.mgf Cmpd 1197, +MSn(759.6966), 115.6 min -1.0 759.69661 3+ 3+ 2276.0560846836997 0 5.228393373659577 0 100.0 Doubtful +11 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 875, +MSn(483.2538), 89.2 min -1.0 483.25374 3+ 3+ 1446.7354586837 0 2.7121200881231644 0 100.0 Doubtful +12 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR tinyspectra.mgf Cmpd 582, +MSn(590.6452), 63.2 min -1.0 590.64518 3+ 3+ 1768.9107986836998 0 1.6433558579610066 0 100.0 Doubtful +13 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 75, +MSn(641.8547), 26.7 min -1.0 641.85466 2+ 2+ 1281.6928656837001 0 1.4811651380377848 0 100.0 Doubtful +14 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 871, +MSn(724.3762), 88.9 min -1.0 724.37624 2+ 2+ 1446.7354586837 0 1.7038016610019715 0 100.0 Doubtful +15 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR tinyspectra.mgf Cmpd 220, +MSn(824.3852), 36.3 min -1.0 824.38516 3+ 3+ 2470.1263816837 0 2.9391347559636922 0 100.0 Doubtful +16 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 591, +MSn(509.9328), 63.7 min -1.0 509.93283 3+ 3+ 1526.7728996836997 0 2.458444778796749 0 100.0 Doubtful +17 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK tinyspectra.mgf Cmpd 736, +MSn(742.0258), 75.1 min -1.0 742.02585 3+ 3+ 2223.0583016837 0 -1.1594749443833878 0 100.0 Doubtful +18 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 72, +MSn(428.2391), 26.6 min -1.0 428.23909 3+ 3+ 1281.6928656837001 0 2.0042705774391996 0 100.0 Doubtful +19 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 588, +MSn(764.3961), 63.5 min -1.0 764.39611 2+ 2+ 1526.7728996836997 0 3.1184077735785474 0 100.0 Doubtful +20 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR tinyspectra.mgf Cmpd 758, +MSn(847.7508), 76.8 min -1.0 847.75082 3+ 3+ 2540.2241966836996 0 2.5298047449054923 0 100.0 Doubtful +21 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK tinyspectra.mgf Cmpd 357, +MSn(687.8723), 46.6 min -1.0 687.87224 2+ 2+ 1373.7336876837 0 -2.733506911277659 0 100.0 Doubtful +22 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK tinyspectra.mgf Cmpd 736, MSn(742.0258), 75.1 min -1.0 742.02585 3+ 3+ 2223.0583016837 0 -1.1594749443833878 0 100.0 Doubtful +23 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR tinyspectra.mgf Cmpd 636, MSn(730.3981), 66.9 min -1.0 730.39814 2+ 2+ 1458.7864506836997 0 -3.233580283650776 0 100.0 Doubtful +24 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 591, MSn(509.9328), 63.7 min -1.0 509.93283 3+ 3+ 1526.7728996836997 0 2.458444778796749 0 100.0 Doubtful +25 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR tinyspectra.mgf Cmpd 39, MSn(594.3056), 25.0 min -1.0 594.30561 2+ 2+ 1186.5942146837 0 2.0632379154490605 0 100.0 Doubtful +26 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR tinyspectra.mgf Cmpd 67, MSn(562.2947), 26.3 min -1.0 562.29468 2+ 2+ 1122.5669286837 0 7.00561302556395 0 100.0 Doubtful +27 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR tinyspectra.mgf Cmpd 752, MSn(697.6842), 76.3 min -1.0 697.68418 3+ 3+ 2090.0167716836995 0 6.659655420038472 0 100.0 Doubtful +28 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 207, MSn(785.9179), 35.7 min -1.0 785.91791 2+ 2+ 1569.8362346836998 0 -9.522288910374096 0 100.0 Doubtful +29 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 875, MSn(483.2538), 89.2 min -1.0 483.25374 3+ 3+ 1446.7354586837 0 2.7121200881231644 0 100.0 Doubtful +30 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 72, MSn(428.2391), 26.6 min -1.0 428.23909 3+ 3+ 1281.6928656837001 0 2.0042705774391996 0 100.0 Doubtful +31 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK tinyspectra.mgf Cmpd 81, MSn(610.3171), 27.0 min -1.0 610.31708 3+ 3+ 1827.9326546837003 0 -1.7717994436305495 0 100.0 Doubtful +32 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR tinyspectra.mgf Cmpd 758, MSn(847.7508), 76.8 min -1.0 847.75082 3+ 3+ 2540.2241966836996 0 2.5298047449054923 0 100.0 Doubtful +33 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 588, MSn(764.3961), 63.5 min -1.0 764.39611 2+ 2+ 1526.7728996836997 0 3.1184077735785474 0 100.0 Doubtful +34 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 871, MSn(724.3762), 88.9 min -1.0 724.37624 2+ 2+ 1446.7354586837 0 1.7038016610019715 0 100.0 Doubtful +35 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK tinyspectra.mgf Cmpd 1197, MSn(759.6966), 115.6 min -1.0 759.69661 3+ 3+ 2276.0560846836997 0 5.228393373659577 0 100.0 Doubtful +36 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 204, MSn(524.2825), 35.5 min -1.0 524.28252 3+ 3+ 1569.8362346836998 0 -6.678342042310128 0 100.0 Doubtful +37 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK tinyspectra.mgf Cmpd 748, MSn(789.0604), 76.1 min -1.0 789.06034 3+ 3+ 2364.1444886837 0 6.210765906697086 0 100.0 Doubtful +38 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR tinyspectra.mgf Cmpd 582, MSn(590.6452), 63.2 min -1.0 590.64518 3+ 3+ 1768.9107986836998 0 1.6433558579610066 0 100.0 Doubtful +39 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 75, MSn(641.8547), 26.7 min -1.0 641.85466 2+ 2+ 1281.6928656837001 0 1.4811651380377848 0 100.0 Doubtful +40 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR tinyspectra.mgf Cmpd 220, MSn(824.3852), 36.3 min -1.0 824.38516 3+ 3+ 2470.1263816837 0 2.9391347559636922 0 100.0 Doubtful +41 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK tinyspectra.mgf Cmpd 357, MSn(687.8723), 46.6 min -1.0 687.87224 2+ 2+ 1373.7336876837 0 -2.733506911277659 0 100.0 Doubtful
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_psm_result2.tabular Mon Feb 16 04:18:17 2015 -0500 @@ -0,0 +1,42 @@ + Protein(s) Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Decoy Localization Confidence probabilistic PTM score D-score Confidence Validation +1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR tinyspectra.mgf Cmpd 752, +MSn(697.6842), 76.3 min -1.0 697.68418 3+ 3+ 2090.0167716836995 0 6.659655420038472 0 100.0 Doubtful +2 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK tinyspectra.mgf Cmpd 748, +MSn(789.0604), 76.1 min -1.0 789.06034 3+ 3+ 2364.1444886837 0 6.210765906697086 0 100.0 Doubtful +3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 204, +MSn(524.2825), 35.5 min -1.0 524.28252 3+ 3+ 1569.8362346836998 0 -6.678342042310128 0 100.0 Doubtful +4 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR tinyspectra.mgf Cmpd 39, +MSn(594.3056), 25.0 min -1.0 594.30561 2+ 2+ 1186.5942146837 0 2.0632379154490605 0 100.0 Doubtful +5 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK tinyspectra.mgf Cmpd 81, +MSn(610.3171), 27.0 min -1.0 610.31708 3+ 3+ 1827.9326546837003 0 -1.7717994436305495 0 100.0 Doubtful +6 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR tinyspectra.mgf Cmpd 636, +MSn(730.3981), 66.9 min -1.0 730.39814 2+ 2+ 1458.7864506836997 0 -3.233580283650776 0 100.0 Doubtful +7 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK tinyspectra.mgf Cmpd 1198, +MSn(1139.0413), 115.6 min -1.0 1139.04127 2+ 2+ 2276.0560846836997 0 5.224764535153943 0 100.0 Doubtful +8 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR tinyspectra.mgf Cmpd 67, +MSn(562.2947), 26.3 min -1.0 562.29468 2+ 2+ 1122.5669286837 0 7.00561302556395 0 100.0 Doubtful +9 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 207, +MSn(785.9179), 35.7 min -1.0 785.91791 2+ 2+ 1569.8362346836998 0 -9.522288910374096 0 100.0 Doubtful +10 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK tinyspectra.mgf Cmpd 1197, +MSn(759.6966), 115.6 min -1.0 759.69661 3+ 3+ 2276.0560846836997 0 5.228393373659577 0 100.0 Doubtful +11 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 875, +MSn(483.2538), 89.2 min -1.0 483.25374 3+ 3+ 1446.7354586837 0 2.7121200881231644 0 100.0 Doubtful +12 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR tinyspectra.mgf Cmpd 582, +MSn(590.6452), 63.2 min -1.0 590.64518 3+ 3+ 1768.9107986836998 0 1.6433558579610066 0 100.0 Doubtful +13 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 75, +MSn(641.8547), 26.7 min -1.0 641.85466 2+ 2+ 1281.6928656837001 0 1.4811651380377848 0 100.0 Doubtful +14 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 871, +MSn(724.3762), 88.9 min -1.0 724.37624 2+ 2+ 1446.7354586837 0 1.7038016610019715 0 100.0 Doubtful +15 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR tinyspectra.mgf Cmpd 220, +MSn(824.3852), 36.3 min -1.0 824.38516 3+ 3+ 2470.1263816837 0 2.9391347559636922 0 100.0 Doubtful +16 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 591, +MSn(509.9328), 63.7 min -1.0 509.93283 3+ 3+ 1526.7728996836997 0 2.458444778796749 0 100.0 Doubtful +17 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK tinyspectra.mgf Cmpd 736, +MSn(742.0258), 75.1 min -1.0 742.02585 3+ 3+ 2223.0583016837 0 -1.1594749443833878 0 100.0 Doubtful +18 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 72, +MSn(428.2391), 26.6 min -1.0 428.23909 3+ 3+ 1281.6928656837001 0 2.0042705774391996 0 100.0 Doubtful +19 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 588, +MSn(764.3961), 63.5 min -1.0 764.39611 2+ 2+ 1526.7728996836997 0 3.1184077735785474 0 100.0 Doubtful +20 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR tinyspectra.mgf Cmpd 758, +MSn(847.7508), 76.8 min -1.0 847.75082 3+ 3+ 2540.2241966836996 0 2.5298047449054923 0 100.0 Doubtful +21 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK tinyspectra.mgf Cmpd 357, +MSn(687.8723), 46.6 min -1.0 687.87224 2+ 2+ 1373.7336876837 0 -2.733506911277659 0 100.0 Doubtful +22 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK tinyspectra.mgf Cmpd 736, MSn(742.0258), 75.1 min -1.0 742.02585 3+ 3+ 2223.0583016837 0 -1.1594749443833878 0 100.0 Doubtful +23 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR tinyspectra.mgf Cmpd 636, MSn(730.3981), 66.9 min -1.0 730.39814 2+ 2+ 1458.7864506836997 0 -3.233580283650776 0 100.0 Doubtful +24 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 591, MSn(509.9328), 63.7 min -1.0 509.93283 3+ 3+ 1526.7728996836997 0 2.458444778796749 0 100.0 Doubtful +25 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR tinyspectra.mgf Cmpd 39, MSn(594.3056), 25.0 min -1.0 594.30561 2+ 2+ 1186.5942146837 0 2.0632379154490605 0 100.0 Doubtful +26 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR tinyspectra.mgf Cmpd 67, MSn(562.2947), 26.3 min -1.0 562.29468 2+ 2+ 1122.5669286837 0 7.00561302556395 0 100.0 Doubtful +27 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR tinyspectra.mgf Cmpd 752, MSn(697.6842), 76.3 min -1.0 697.68418 3+ 3+ 2090.0167716836995 0 6.659655420038472 0 100.0 Doubtful +28 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 207, MSn(785.9179), 35.7 min -1.0 785.91791 2+ 2+ 1569.8362346836998 0 -9.522288910374096 0 100.0 Doubtful +29 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 875, MSn(483.2538), 89.2 min -1.0 483.25374 3+ 3+ 1446.7354586837 0 2.7121200881231644 0 100.0 Doubtful +30 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 72, MSn(428.2391), 26.6 min -1.0 428.23909 3+ 3+ 1281.6928656837001 0 2.0042705774391996 0 100.0 Doubtful +31 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK tinyspectra.mgf Cmpd 81, MSn(610.3171), 27.0 min -1.0 610.31708 3+ 3+ 1827.9326546837003 0 -1.7717994436305495 0 100.0 Doubtful +32 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR tinyspectra.mgf Cmpd 758, MSn(847.7508), 76.8 min -1.0 847.75082 3+ 3+ 2540.2241966836996 0 2.5298047449054923 0 100.0 Doubtful +33 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR tinyspectra.mgf Cmpd 588, MSn(764.3961), 63.5 min -1.0 764.39611 2+ 2+ 1526.7728996836997 0 3.1184077735785474 0 100.0 Doubtful +34 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR tinyspectra.mgf Cmpd 871, MSn(724.3762), 88.9 min -1.0 724.37624 2+ 2+ 1446.7354586837 0 1.7038016610019715 0 100.0 Doubtful +35 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK tinyspectra.mgf Cmpd 1197, MSn(759.6966), 115.6 min -1.0 759.69661 3+ 3+ 2276.0560846836997 0 5.228393373659577 0 100.0 Doubtful +36 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK tinyspectra.mgf Cmpd 204, MSn(524.2825), 35.5 min -1.0 524.28252 3+ 3+ 1569.8362346836998 0 -6.678342042310128 0 100.0 Doubtful +37 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK tinyspectra.mgf Cmpd 748, MSn(789.0604), 76.1 min -1.0 789.06034 3+ 3+ 2364.1444886837 0 6.210765906697086 0 100.0 Doubtful +38 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR tinyspectra.mgf Cmpd 582, MSn(590.6452), 63.2 min -1.0 590.64518 3+ 3+ 1768.9107986836998 0 1.6433558579610066 0 100.0 Doubtful +39 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK tinyspectra.mgf Cmpd 75, MSn(641.8547), 26.7 min -1.0 641.85466 2+ 2+ 1281.6928656837001 0 1.4811651380377848 0 100.0 Doubtful +40 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR tinyspectra.mgf Cmpd 220, MSn(824.3852), 36.3 min -1.0 824.38516 3+ 3+ 2470.1263816837 0 2.9391347559636922 0 100.0 Doubtful +41 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK tinyspectra.mgf Cmpd 357, MSn(687.8723), 46.6 min -1.0 687.87224 2+ 2+ 1373.7336876837 0 -2.733506911277659 0 100.0 Doubtful
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/searchgui_tinydb1.fasta Mon Feb 16 04:18:17 2015 -0500 @@ -0,0 +1,24 @@ +>cds.comp107265_c0_seq1|m.36816 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.94 EValue:9.0e-68 +LKSSFESSFSIKSRDVTFGNSMNITMVPPELEFFKDNRHKEKSEMQDLNTRLESYLSVGKDDSDANLKLMQELEEIKNGIKTETNNIKATFEAELGQLKNLLDDIDHDKNQVIVIGDNNDEMYKDLEQRIKNYNDMEMIHLSKIRQLDNLLSNYGLKMNQLQKKIGFLCEEKDRDIESINKLRADIDVAKNDLSNEILLRTDAQNRCQSLEEDIEFTKEVHQRELSNMIALADYDPVSQSMDWWNDEFARCIKEIQDEYEDRLNNIQYDMDSHYNSKIQDVETTILQSSAKSEMLDQCSMLENSNAEIEDQTSELEKKNAMLKEQNDLLNRGIREIQSQFETLITEKQSEMLEIRKHFEQSLADLQAIVDDNLSLQMEIMSYKKLLECEELRVGIYPESNANENQGDQGQRQNEQITEPITETIPKRKKPERKISYQRSSKGPLTISECKSDGSYILIENMDQYDGQNLGGWRLVQNVDGMEEYDYTFSRYYLGPGESVKIWAENAGPKGVNDLVWDDLKCLGIGEKVITSLMNQKGKEKSSYTQKAIYKV +>cds.comp307584_c0_seq2|m.40556 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 39.47 EValue:1.0e-14 +DDNYDSLQYSFPKSDHQRKTTYQRSAKGPITITRVQPDGSYIEIENTNIAVNEDISGWKMVQCTDDKIYEYIFDDHVLNGGTCVKIWANGLSGKEENDLVWIDRTCLTTGSVVTTTLMDYNGNEKATFTQ +>cds.comp376950_c0_seq1|m.42080 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 41.38 EValue:1.0e-32 +KELEDINEDNLGRLRRQDEDVSNYEAQNASLRRKCDNLQADKDRDRNNVEKLKGEVTSLRNDLMMETVSRIDSQNKCQTLREELEFLKDIHSQELKELSPTLGKDPFAKSKEWWSSEFSNCIREIQEEYDNRLDSIKTDMDNYYTLKVQEIQTGAAR +>cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67 +METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT +>cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 +METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT +>cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 +SGLAGDSDTMRASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT +>cds.comp41890_c0_seq1|m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20 +YQSPTPALVKGELQEHSTYRKNNKGPVAISETDRDGSFILLENTSNSHTVDLSGWKIMQNSDNIDISEYEIENLVLKPGGFAKVWANGMGDPNSGDLVWHNKSRLGVGAKVNTVLLNTRGDEKATYNLETTYNL +>cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91 +MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGTTSITTGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF +>cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 +MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF +>cds.comp55448_c0_seq1|m.24261 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 96.04 EValue:0.0 +MRRIKKKITLDVRVTELIDQLERQQKELEESRTYHQIDQEQIARQNQQLADLEGEISMLRRSIESLEKEKMRQSNILAKMNDELEKLRMDLNNETINHLDAENRRQTLEEELEFQKDVHAQELKELAALAYRDTTAENREFWRNELAQAIRDIQQEYDAKCDQMRGDIEAYYNLKVQEFRTGATKQNMEVTRNKEENTKLRSNMNEVRNRLADLEARNAQLERTNQDLLRDLEEKDRQNELESCQYKEEITKLRGEMESILKELQDLMDIKLSLELEIAAYRKLLEGEESRVGMKQIVEQVVGARPNEAEVLSSILTRSEGGYEATGDSQISMKMMRGELAAKTTYQRTSKGPVSIKEADSQGQFIALETKKEENITGWKIVRKVDDNMVYSYEIPNVVLKTGTVIKIWSKSHQAQARGDDIVSRENDTWGTGSNVVTILQNEKGEEKANYTQNTVYQ +>cds.comp55448_c0_seq1|m.24262 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 91.49 EValue:5.0e-87 +MSGGFSYSAKIHPRTGYVSRTSQSPYRSSMGSNAAFTRSYEFNYGATAMPGAYANISSTGVNHVKANREREKQDMRDLNERFANYIEKVRFLEAQNKKLAGELEELKSKWGKETSAIKEMYETELEEARKLIDATNKEKNYLGRESN +>cds.comp8310_c0_seq2|m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16 +FKDTCIRDKTDMKGLNERLSEFIEVARYNAILAKKLEKTIKRFHSQEIPEDVERIYEATIKKLRKLLVVFENERDNERAKNLKLQTECAKLKESLEDLKAKEIENRDRLISKFKILEDLQSKAIRIEKNIEIVAEENVLKNNKIEKLKKHFENLKSKITSERRNRSTHKESYDEVKEDFGIFKELKNQQLSSVRFPKYKDSIKYLRKQWSNEFSKCIKELQNEYESRVSSVKEELESNYCTKTEEIQNYVLKSNYESDFLKNRNLVAEESMNMLKNKFKEAKKENVLLNHEKEELEIEFNKSKNEYDHLAEEKNNEILNFKEYAEKILIQLTEILEINNHLQFEIEYYKTVITSGETKIDFDFDGLDDECMTSINSELP
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/searchgui_tinyspectra1.mgf Mon Feb 16 04:18:17 2015 -0500 @@ -0,0 +1,6153 @@ +BEGIN IONS +TITLE= Cmpd 636, +MSn(730.3981), 66.9 min +PEPMASS=730.39814 92569 +CHARGE=2+ +156.06738 122 +175.10440 1049 +186.08322 120 +187.12501 241 +188.06515 494 1+ +193.09503 180 +197.12522 208 +199.17309 1374 1+ +204.08687 454 1+ +213.14347 128 +215.11998 747 1+ +227.17167 1524 1+ +229.12416 156 +233.09327 3574 1+ +236.99586 113 +243.14264 571 1+ +244.07481 236 +245.12901 240 +246.12647 275 +256.20038 432 1+ +258.12496 133 +260.19976 423 +261.09190 17853 1+ +270.16206 114 +274.12614 207 +283.15366 136 +284.18559 406 1+ +286.14626 237 +287.10013 105 +301.15759 131 +303.17924 2962 1+ +310.21264 944 1+ +315.13250 122 +316.16696 108 +326.16601 145 +328.21268 874 1+ +335.13393 406 1+ +338.20704 186 +339.16449 110 +342.17857 106 +344.13585 148 +346.17426 809 1+ +356.21762 685 1+ +358.15839 265 +359.26213 106 +362.14671 528 1+ +366.16564 103 +370.14930 136 +374.17893 18824 1+ +380.20460 141 +384.22488 193 +387.21562 161 +388.26191 188 +411.26204 166 +415.22868 119 +416.26432 2092 1+ +421.21633 119 +423.29102 378 1+ +425.19591 120 +429.24479 213 +430.23711 292 +431.20421 187 +436.18404 103 +436.75217 164 +437.24576 210 +439.24189 686 1+ +441.27348 282 +442.22757 266 +443.24151 187 +447.25851 136 +448.23776 110 +451.24187 133 +454.21183 186 +455.28038 426 1+ +457.22899 1666 1+ +459.26367 3533 1+ +470.24566 153 +471.25916 214 +472.22369 149 +475.22776 2402 1+ +476.74146 108 +478.76406 148 +479.26444 182 +481.79718 109 +482.23965 265 +484.28349 122 +485.26864 194 +487.26385 8530 1+ +487.76699 2322 2+ +492.79121 214 +493.27987 223 +496.25943 155 +498.26458 113 +499.26123 188 +500.25926 116 +502.31880 144 +503.29803 113 +505.25694 134 +507.23129 148 +509.26114 112 +512.29082 270 +516.25599 158 +517.20915 133 +517.28047 196 +518.26358 209 +519.25298 141 +524.32901 134 +525.28341 246 +525.73648 129 +526.28178 183 +527.27825 442 1+ +530.27675 144 +531.28549 121 +533.28116 104 +534.11078 105 +534.80853 658 2+ +536.27223 192 +537.26164 134 +538.59905 107 +539.27286 106 +540.27423 189 +541.25963 119 +542.30271 822 1+ +543.81900 3982 2+ +544.31230 3061 1+ +546.73644 112 +550.76990 117 +551.22357 107 +552.32208 662 1+ +555.31596 235 +556.27474 176 +558.29453 154 +559.29947 142 +560.30729 1143 1+ +567.24429 116 +569.25892 228 +570.29732 7469 1+ +575.31645 290 +580.32039 169 +584.32568 221 +585.29844 155 +588.30437 6069 1+ +591.34398 1900 2+ +593.19489 103 +594.32473 103 +598.30327 171 +600.36464 3642 2+ +602.30487 970 1+ +608.28169 160 +609.27493 133 +614.83731 112 +615.27771 193 +617.30438 138 +618.32896 149 +619.33485 160 +620.31542 115 +620.81406 230 +622.32210 208 +623.32017 135 +624.28638 129 +626.34792 207 +628.34041 189 +629.25299 114 +630.37407 171 +632.31114 124 +634.29651 120 +636.28359 105 +637.35608 222 +638.34750 245 +639.34410 173 +641.33612 839 1+ +646.33654 117 +647.19559 1433 1+ +649.19722 1100 1+ +651.31229 136 +653.31813 227 +654.33373 187 +655.38010 176 +656.35127 649 1+ +658.36493 6652 1+ +664.87410 264 +665.36702 578 1+ +668.36277 108 +669.88900 118 +671.36838 605 1+ +673.38354 533 1+ +674.31604 138 +680.33315 119 +682.86635 152 +683.37863 4557 1+ +689.35741 806 1+ +693.34598 140 +695.38537 116 +696.37550 112 +697.39934 146 +698.39359 132 +699.36352 115 +701.38282 1437 1+ +706.39934 164 +707.37693 151 +707.86433 178 +710.37380 213 +712.37982 250 +712.89070 251 +713.37280 260 +713.88658 123 +715.37058 153 +716.18442 4201 1+ +716.77672 108 +718.18321 2451 1+ +718.88287 2231 2+ +720.98962 121 +721.39031 3707 2+ +724.88574 175 +725.39311 174 +725.86419 119 +726.38179 168 +726.88029 279 +727.39635 1151 2+ +729.38218 580 +729.89636 3472 1+ +730.39870 7202 2+ +733.22310 218 +733.30736 209 +733.86699 2221 2+ +734.87807 2000 2+ +737.41263 157 +738.38323 548 1+ +741.39676 215 +742.38824 893 1+ +748.42865 106 +757.40883 110 +759.41390 16956 1+ +766.39835 135 +768.40610 123 +773.41497 135 +775.43074 138 +779.38031 110 +784.42558 899 1+ +787.90750 114 +788.43303 156 +802.43422 958 1+ +818.92372 110 +819.43952 106 +830.50628 147 +838.45103 121 +855.49252 207 +866.39951 113 +872.50085 6571 1+ +880.44367 148 +886.46997 133 +891.44688 208 +899.47954 151 +912.47926 133 +914.49331 112 +916.46838 134 +924.48363 139 +926.42073 111 +955.52131 165 +956.52827 785 1+ +973.55087 13950 1+ +978.51217 225 +979.51564 116 +980.49756 186 +1008.48933 103 +1044.54839 219 +1068.60979 255 1+ +1086.63071 4224 1+ +1187.60270 135 +1199.72200 1064 1+ +END IONS + +BEGIN IONS +TITLE= Cmpd 67, +MSn(562.2947), 26.3 min +PEPMASS=562.29468 458049 +CHARGE=2+ +173.10446 888 +175.10614 7500 1+ +179.03885 2115 1+ +181.05013 1444 +185.10363 748 +188.09581 546 +189.08230 1123 +191.10888 1205 +193.08988 20362 1+ +197.12012 1004 +198.08421 1715 +199.08156 3683 1+ +201.11270 1482 +202.08307 5961 1+ +204.12828 1144 +207.10914 5879 1+ +212.09747 547 +214.14801 786 +215.13458 1085 +216.09374 15154 1+ +219.10360 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--- a/test-data/tinydb.fasta Mon Dec 15 21:33:25 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ ->cds.comp107265_c0_seq1|m.36816 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.94 EValue:9.0e-68 -LKSSFESSFSIKSRDVTFGNSMNITMVPPELEFFKDNRHKEKSEMQDLNTRLESYLSVGKDDSDANLKLMQELEEIKNGIKTETNNIKATFEAELGQLKNLLDDIDHDKNQVIVIGDNNDEMYKDLEQRIKNYNDMEMIHLSKIRQLDNLLSNYGLKMNQLQKKIGFLCEEKDRDIESINKLRADIDVAKNDLSNEILLRTDAQNRCQSLEEDIEFTKEVHQRELSNMIALADYDPVSQSMDWWNDEFARCIKEIQDEYEDRLNNIQYDMDSHYNSKIQDVETTILQSSAKSEMLDQCSMLENSNAEIEDQTSELEKKNAMLKEQNDLLNRGIREIQSQFETLITEKQSEMLEIRKHFEQSLADLQAIVDDNLSLQMEIMSYKKLLECEELRVGIYPESNANENQGDQGQRQNEQITEPITETIPKRKKPERKISYQRSSKGPLTISECKSDGSYILIENMDQYDGQNLGGWRLVQNVDGMEEYDYTFSRYYLGPGESVKIWAENAGPKGVNDLVWDDLKCLGIGEKVITSLMNQKGKEKSSYTQKAIYKV ->cds.comp307584_c0_seq2|m.40556 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 39.47 EValue:1.0e-14 -DDNYDSLQYSFPKSDHQRKTTYQRSAKGPITITRVQPDGSYIEIENTNIAVNEDISGWKMVQCTDDKIYEYIFDDHVLNGGTCVKIWANGLSGKEENDLVWIDRTCLTTGSVVTTTLMDYNGNEKATFTQ ->cds.comp376950_c0_seq1|m.42080 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 41.38 EValue:1.0e-32 -KELEDINEDNLGRLRRQDEDVSNYEAQNASLRRKCDNLQADKDRDRNNVEKLKGEVTSLRNDLMMETVSRIDSQNKCQTLREELEFLKDIHSQELKELSPTLGKDPFAKSKEWWSSEFSNCIREIQEEYDNRLDSIKTDMDNYYTLKVQEIQTGAAR ->cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67 -METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT ->cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 -METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT ->cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 -SGLAGDSDTMRASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT ->cds.comp41890_c0_seq1|m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20 -YQSPTPALVKGELQEHSTYRKNNKGPVAISETDRDGSFILLENTSNSHTVDLSGWKIMQNSDNIDISEYEIENLVLKPGGFAKVWANGMGDPNSGDLVWHNKSRLGVGAKVNTVLLNTRGDEKATYNLETTYNL ->cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91 -MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGTTSITTGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF ->cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 -MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF ->cds.comp55448_c0_seq1|m.24261 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 96.04 EValue:0.0 -MRRIKKKITLDVRVTELIDQLERQQKELEESRTYHQIDQEQIARQNQQLADLEGEISMLRRSIESLEKEKMRQSNILAKMNDELEKLRMDLNNETINHLDAENRRQTLEEELEFQKDVHAQELKELAALAYRDTTAENREFWRNELAQAIRDIQQEYDAKCDQMRGDIEAYYNLKVQEFRTGATKQNMEVTRNKEENTKLRSNMNEVRNRLADLEARNAQLERTNQDLLRDLEEKDRQNELESCQYKEEITKLRGEMESILKELQDLMDIKLSLELEIAAYRKLLEGEESRVGMKQIVEQVVGARPNEAEVLSSILTRSEGGYEATGDSQISMKMMRGELAAKTTYQRTSKGPVSIKEADSQGQFIALETKKEENITGWKIVRKVDDNMVYSYEIPNVVLKTGTVIKIWSKSHQAQARGDDIVSRENDTWGTGSNVVTILQNEKGEEKANYTQNTVYQ ->cds.comp55448_c0_seq1|m.24262 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 91.49 EValue:5.0e-87 -MSGGFSYSAKIHPRTGYVSRTSQSPYRSSMGSNAAFTRSYEFNYGATAMPGAYANISSTGVNHVKANREREKQDMRDLNERFANYIEKVRFLEAQNKKLAGELEELKSKWGKETSAIKEMYETELEEARKLIDATNKEKNYLGRESN ->cds.comp8310_c0_seq2|m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16 -FKDTCIRDKTDMKGLNERLSEFIEVARYNAILAKKLEKTIKRFHSQEIPEDVERIYEATIKKLRKLLVVFENERDNERAKNLKLQTECAKLKESLEDLKAKEIENRDRLISKFKILEDLQSKAIRIEKNIEIVAEENVLKNNKIEKLKKHFENLKSKITSERRNRSTHKESYDEVKEDFGIFKELKNQQLSSVRFPKYKDSIKYLRKQWSNEFSKCIKELQNEYESRVSSVKEELESNYCTKTEEIQNYVLKSNYESDFLKNRNLVAEESMNMLKNKFKEAKKENVLLNHEKEELEIEFNKSKNEYDHLAEEKNNEILNFKEYAEKILIQLTEILEINNHLQFEIEYYKTVITSGETKIDFDFDGLDDECMTSINSELP
--- a/test-data/tinyspectra.mgf Mon Dec 15 21:33:25 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6153 +0,0 @@ -BEGIN IONS -TITLE= Cmpd 636, +MSn(730.3981), 66.9 min -PEPMASS=730.39814 92569 -CHARGE=2+ -156.06738 122 -175.10440 1049 -186.08322 120 -187.12501 241 -188.06515 494 1+ -193.09503 180 -197.12522 208 -199.17309 1374 1+ -204.08687 454 1+ -213.14347 128 -215.11998 747 1+ -227.17167 1524 1+ -229.12416 156 -233.09327 3574 1+ -236.99586 113 -243.14264 571 1+ -244.07481 236 -245.12901 240 -246.12647 275 -256.20038 432 1+ -258.12496 133 -260.19976 423 -261.09190 17853 1+ -270.16206 114 -274.12614 207 -283.15366 136 -284.18559 406 1+ -286.14626 237 -287.10013 105 -301.15759 131 -303.17924 2962 1+ -310.21264 944 1+ -315.13250 122 -316.16696 108 -326.16601 145 -328.21268 874 1+ -335.13393 406 1+ -338.20704 186 -339.16449 110 -342.17857 106 -344.13585 148 -346.17426 809 1+ -356.21762 685 1+ -358.15839 265 -359.26213 106 -362.14671 528 1+ -366.16564 103 -370.14930 136 -374.17893 18824 1+ -380.20460 141 -384.22488 193 -387.21562 161 -388.26191 188 -411.26204 166 -415.22868 119 -416.26432 2092 1+ -421.21633 119 -423.29102 378 1+ -425.19591 120 -429.24479 213 -430.23711 292 -431.20421 187 -436.18404 103 -436.75217 164 -437.24576 210 -439.24189 686 1+ -441.27348 282 -442.22757 266 -443.24151 187 -447.25851 136 -448.23776 110 -451.24187 133 -454.21183 186 -455.28038 426 1+ -457.22899 1666 1+ -459.26367 3533 1+ -470.24566 153 -471.25916 214 -472.22369 149 -475.22776 2402 1+ -476.74146 108 -478.76406 148 -479.26444 182 -481.79718 109 -482.23965 265 -484.28349 122 -485.26864 194 -487.26385 8530 1+ -487.76699 2322 2+ -492.79121 214 -493.27987 223 -496.25943 155 -498.26458 113 -499.26123 188 -500.25926 116 -502.31880 144 -503.29803 113 -505.25694 134 -507.23129 148 -509.26114 112 -512.29082 270 -516.25599 158 -517.20915 133 -517.28047 196 -518.26358 209 -519.25298 141 -524.32901 134 -525.28341 246 -525.73648 129 -526.28178 183 -527.27825 442 1+ -530.27675 144 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138 -779.38031 110 -784.42558 899 1+ -787.90750 114 -788.43303 156 -802.43422 958 1+ -818.92372 110 -819.43952 106 -830.50628 147 -838.45103 121 -855.49252 207 -866.39951 113 -872.50085 6571 1+ -880.44367 148 -886.46997 133 -891.44688 208 -899.47954 151 -912.47926 133 -914.49331 112 -916.46838 134 -924.48363 139 -926.42073 111 -955.52131 165 -956.52827 785 1+ -973.55087 13950 1+ -978.51217 225 -979.51564 116 -980.49756 186 -1008.48933 103 -1044.54839 219 -1068.60979 255 1+ -1086.63071 4224 1+ -1187.60270 135 -1199.72200 1064 1+ -END IONS - -BEGIN IONS -TITLE= Cmpd 67, +MSn(562.2947), 26.3 min -PEPMASS=562.29468 458049 -CHARGE=2+ -173.10446 888 -175.10614 7500 1+ -179.03885 2115 1+ -181.05013 1444 -185.10363 748 -188.09581 546 -189.08230 1123 -191.10888 1205 -193.08988 20362 1+ -197.12012 1004 -198.08421 1715 -199.08156 3683 1+ -201.11270 1482 -202.08307 5961 1+ -204.12828 1144 -207.10914 5879 1+ -212.09747 547 -214.14801 786 -215.13458 1085 -216.09374 15154 1+ -219.10360 3767 1+ 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--- a/tool_dependencies.xml Mon Dec 15 21:33:25 2014 -0500 +++ b/tool_dependencies.xml Mon Feb 16 04:18:17 2015 -0500 @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> - <package name="searchgui" version="1.23"> - <repository changeset_revision="c3f36ea6ecd8" name="package_searchgui_1_23" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="searchgui" version="1.24"> + <repository changeset_revision="9fa78a2fd80c" name="package_searchgui_1_24" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="peptide_shaker" version="0.35"> - <repository changeset_revision="51996a518b20" name="package_peptideshaker_0_35" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="peptide_shaker" version="0.37"> + <repository changeset_revision="d8ac9d6143ca" name="package_peptideshaker_0_37" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>