Mercurial > repos > galaxyp > pepquery2
changeset 0:3c45645197f6 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
| author | galaxyp |
|---|---|
| date | Wed, 28 Sep 2022 13:56:01 +0000 |
| parents | |
| children | 6b5ce9e2b0d0 |
| files | macros.xml pepquery2.xml |
| diffstat | 2 files changed, 2176 insertions(+), 0 deletions(-) [+] |
line wrap: on
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Sep 28 13:56:01 2022 +0000 @@ -0,0 +1,1245 @@ + <macros> + <token name="@TOOL_VERSION@">2.0.2</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="citations"> + <citations> + <citation type="doi">10.1101/gr.235028.118</citation> + <citation type="doi">10.1038/s41467-020-15456-w</citation> + </citations> + </xml> + <token name="@PEPQUERY_DOCUMANTATION_URL@">http://pepquery.org/document.html</token> + + <token name="@CMD_IMPORTS@"> +#import re +#import os.path +#def identifier_or_name($input1) + #if hasattr($input1, 'element_identifier') + #return $input1.element_identifier + #else + #return $input1.name + #end if +#end def +#def clean($name1) + #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fas|fasta|imzml|mzml|mzxml|mgf|raw)$','', $re.sub('.*/','', $name1.rstrip('.gz')))) + #return $name_clean +#end def +#def ln_name($ds) + #set $ext = '' + #if $ds.is_of_type('mzml') or $ds.is_of_type('imzml') + #set $ext = ".mzML" + #else if $ds.is_of_type('mzxml') + #set $ext = ".mzXML" + #else if $ds.is_of_type('mgf') + #set $ext = ".mgf" + #else if $ds.is_of_type('thermo.raw') + #set $ext = ".raw" + #else if $ds.is_of_type('fasta') + #set $ext = ".fasta" + #end if + #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext) + #return $name +#end def + </token> + + <token name="@INDEX_SPECTRUM_FILES@"><![CDATA[ +#def index_spectrum_files($idx_dir,$spectrum_files) +#set global $input_dir = 'input_dir' +#set global $index_dir = 'index_dir' +mkdir -p $input_dir && +#if $idx_dir +mkdir -p $idx_dir && +ln -s $idx_dir $index_dir && +#else +mkdir -p $index_dir && +#end if +#if isinstance($spectrum_files, list) + #set $sfiles = $spectrum_files +#else + #set $sfiles = [$spectrum_files] +#end if +#for $sf in $sfiles + #set $i_name = $ln_name($sf) + #set $p_name = $os.path.join($input_dir, $i_name) + ln -s '$sf' '$p_name' && +#end for +pepquery index -i input_dir -o index_dir +#end def + ]]></token> + + + <xml name="modifications"> + <option value="0">0: NO Modifications</option> + <option value="1">1: Carbamidomethylation of C [57.02146372057]</option> + <option value="2">2: Oxidation of M [15.99491461956]</option> + <option value="3">3: Deamidation of N [0.9840155826899988]</option> + <option value="4">4: Deamidation of Q [0.9840155826899988]</option> + <option value="5">5: Acetylation of peptide N-term [42.0105646837]</option> + <option value="6">6: Acetylation of K [42.0105646837]</option> + <option value="7">7: Phosphorylation of S [79.96633052074999]</option> + <option value="8">8: Phosphorylation of T [79.96633052074999]</option> + <option value="9">9: Phosphorylation of Y [79.96633052074999]</option> + <option value="10">10: Ubiquitination of K [114.04292744114]</option> + <option value="11">11: TMT 10-plex of K [229.16293213472]</option> + <option value="12">12: TMT 10-plex of peptide N-term [229.16293213472]</option> + <option value="13">13: TMT 11-plex of K [229.16293213472]</option> + <option value="14">14: TMT 11-plex of peptide N-term [229.16293213472]</option> + <option value="15">15: TMT 6-plex of K [229.16293213472]</option> + <option value="16">16: TMT 6-plex of peptide N-term [229.16293213472]</option> + <option value="17">17: TMT 2-plex of K [225.15583272792]</option> + <option value="18">18: TMT 2-plex of peptide N-term [225.15583272792]</option> + <option value="19">19: TMTpro of K [304.20714532623]</option> + <option value="20">20: TMTpro of peptide N-term [304.20714532623]</option> + <option value="21">21: iTRAQ 4-plex of K [144.1020624208]</option> + <option value="22">22: iTRAQ 4-plex of peptide N-term [144.1020624208]</option> + <option value="23">23: iTRAQ 4-plex of Y [144.1020624208]</option> + <option value="24">24: iTRAQ 8-plex of K [304.19903946116]</option> + <option value="25">25: iTRAQ 8-plex of peptide N-term [304.19903946116]</option> + <option value="26">26: iTRAQ 8-plex of Y [304.19903946116]</option> + <option value="27">27: Pyrolidone from E [-18.0105646837]</option> + <option value="28">28: Pyrolidone from Q [-17.02654910101]</option> + <option value="29">29: 18O(1) of peptide C-term [2.0042463804400015]</option> + <option value="30">30: 18O(2) of peptide C-term [4.008492760880003]</option> + <option value="31">31: 4-Hydroxyproline [83.07349929343) -</option> + <option value="32">32: Acetaldehyde +26 [26.01565006414]</option> + <option value="33">33: Acetylation of protein N-term [42.0105646837]</option> + <option value="34">34: ADP-ribosylation of S [541.06110901175]</option> + <option value="35">35: Amidation of peptide C-term [-0.9840155826899988]</option> + <option value="36">36: Amidation of protein C-term [-0.9840155826899988]</option> + <option value="37">37: Ammonia loss from N [-17.02654910101]</option> + <option value="38">38: Arginine 13C(6) [6.020129026799992]</option> + <option value="39">39: Arginine 13C(6) 15N(4) [10.008268600400015]</option> + <option value="40">40: Biotinylation of K [226.0775986977]</option> + <option value="41">41: Butyrylation of K [70.04186481197999]</option> + <option value="42">42: Calcium on D [37.94694080186]</option> + <option value="43">43: Calcium on E [37.94694080186]</option> + <option value="44">44: Carbamidomethylation of E [57.02146372057]</option> + <option value="45">45: Carbamidomethylation of K [57.02146372057]</option> + <option value="46">46: Carbamilation of C [43.00581365643]</option> + <option value="47">47: Carbamilation of K [43.00581365643]</option> + <option value="48">48: Carbamilation of M [43.00581365643]</option> + <option value="49">49: Carbamilation of protein N-term [43.00581365643]</option> + <option value="50">50: Carbamilation of R [43.00581365643]</option> + <option value="51">51: Carboxylation of D [43.98982923912]</option> + <option value="52">52: Carboxylation of E [43.98982923912]</option> + <option value="53">53: Carboxylation of K [43.98982923912]</option> + <option value="54">54: Carboxymethylation of C [58.00547930326]</option> + <option value="55">55: Carboxymethylation of K [58.00547930326]</option> + <option value="56">56: Carboxymethylation of peptide N-term [58.00547930326]</option> + <option value="57">57: Carboxymethylation of W [58.00547930326]</option> + <option value="58">58: Citrullination of R [0.9840155826899988]</option> + <option value="59">59: Copper on D [61.92177246793]</option> + <option value="60">60: Copper on E [61.92177246793]</option> + <option value="61">61: Crotonylation of K [68.02621474784]</option> + <option value="62">62: Deamidation of N 18O [2.9882619631300003]</option> + <option value="63">63: Dehydration of S [-18.0105646837]</option> + <option value="64">64: Dehydration of T [-18.0105646837]</option> + <option value="65">65: Didehydro of T [-2.01565006414]</option> + <option value="66">66: Didehydro of Y [-2.01565006414]</option> + <option value="67">67: Diiodination of Y [251.79329593586]</option> + <option value="68">68: Dimethylation of K [28.03130012828]</option> + <option value="69">69: Dimethylation of K 2H(4) [32.0564071112]</option> + <option value="70">70: Dimethylation of K 2H(6) [34.068960602660006]</option> + <option value="71">71: Dimethylation of K 2H(6) 13C(2) [36.075670278260006]</option> + <option value="72">72: Dimethylation of N [28.03130012828]</option> + <option value="73">73: Dimethylation of peptide N-term [28.03130012828]</option> + <option value="74">74: Dimethylation of peptide N-term 2H(4) [32.0564071112]</option> + <option value="75">75: Dimethylation of peptide N-term 2H(6) [34.068960602660006]</option> + <option value="76">76: Dimethylation of peptide N-term 2H(6) 13C(2) [36.075670278260006]</option> + <option value="77">77: Dimethylation of R [28.03130012828]</option> + <option value="78">78: Dioxidation of M [31.98982923912]</option> + <option value="79">79: Dioxidation of W [31.98982923912]</option> + <option value="80">80: Farnesylation of C [204.18780076968]</option> + <option value="81">81: Formylation of K [27.99491461956]</option> + <option value="82">82: Formylation of peptide N-term [27.99491461956]</option> + <option value="83">83: Formylation of protein N-term [27.99491461956]</option> + <option value="84">84: Formylation of S [27.99491461956]</option> + <option value="85">85: Formylation of T [27.99491461956]</option> + <option value="86">86: FormylMet of protein N-term [159.03539953255]</option> + <option value="87">87: Geranyl-geranyl of C [272.25040102624]</option> + <option value="88">88: Glutarylation of K [114.0316940511]</option> + <option value="89">89: Glutathione of C [305.06815621281]</option> + <option value="90">90: Guanidination of K [42.02179807374]</option> + <option value="91">91: Guanidination of peptide N-term [42.02179807374]</option> + <option value="92">92: Heme B of C [616.17729182368]</option> + <option value="93">93: Heme B of H [616.17729182368]</option> + <option value="94">94: Hex(1)NAc(1) of S [365.13219593801]</option> + <option value="95">95: Hex(1)NAc(1) of T [365.13219593801]</option> + <option value="96">96: Hex(5) HexNAc(4) NeuAc(2) Na of N [2226.75438443231]</option> + <option value="97">97: Hex(5) HexNAc(4) NeuAc(2) of N [2204.77244018348) -</option> + <option value="98">98: HexNAc of S [203.07937251951]</option> + <option value="99">99: HexNAc of T [203.07937251951]</option> + <option value="100">100: Hexose of K [162.0528234185]</option> + <option value="101">101: Homoserine lactone of peptide C-term M [-48.00337112828]</option> + <option value="102">102: Homoserine of peptide C-term M [-29.992806444580005]</option> + <option value="103">103: ICAT-9 [236.15718495847]</option> + <option value="104">104: ICAT-O [227.12699141827]</option> + <option value="105">105: ICPL0 of K [105.02146372057]</option> + <option value="106">106: ICPL0 of peptide N-term [105.02146372057]</option> + <option value="107">107: ICPL10 of K [115.06669973029]</option> + <option value="108">108: ICPL10 of peptide N-term [115.06669973029]</option> + <option value="109">109: ICPL4 of K [109.04657070349]</option> + <option value="110">110: ICPL4 of peptide N-term [109.04657070349]</option> + <option value="111">111: ICPL6 of K [111.04159274737]</option> + <option value="112">112: ICPL6 of peptide N-term [111.04159274737]</option> + <option value="113">113: iodoTMT 6-plex of C [329.22659502044]</option> + <option value="114">114: iodoTMT zero of C [324.21614077584]</option> + <option value="115">115: Iron[II] on D [53.91928623586]</option> + <option value="116">116: Iron[II] on E [53.91928623586]</option> + <option value="117">117: Iron[III] on D [52.91146120379]</option> + <option value="118">118: Iron[III] on E [52.91146120379]</option> + <option value="119">119: Isoleucine 13C(6) 15N(1) [7.017163920200005]</option> + <option value="120">120: Label of K 2H(4) [4.025106982920001]</option> + <option value="121">121: Leucine 13C(6) 15N(1) [7.017163920200005]</option> + <option value="122">122: Lipoyl of K [188.0329570044]</option> + <option value="123">123: Lysine 13C(6) [6.020129026799992]</option> + <option value="124">124: Lysine 13C(6) 15N(2) [8.014198813600004]</option> + <option value="125">125: Lysine 2H(4) [4.025106982920001]</option> + <option value="126">126: Magnesium on D [21.96939163286]</option> + <option value="127">127: Magnesium on E [21.96939163286]</option> + <option value="128">128: Malonylation of K [86.00039392282]</option> + <option value="129">129: Methylation of C [14.01565006414]</option> + <option value="130">130: Methylation of D [14.01565006414]</option> + <option value="131">131: Methylation of E [14.01565006414]</option> + <option value="132">132: Methylation of K [14.01565006414]</option> + <option value="133">133: Methylation of R [14.01565006414]</option> + <option value="134">134: Methylation of S [14.01565006414]</option> + <option value="135">135: Methylthio of C [45.987721064140004]</option> + <option value="136">136: Methylthio of D [45.987721064140004]</option> + <option value="137">137: Methylthio of N [45.987721064140004]</option> + <option value="138">138: mTRAQ of 13C(6) 15N(2) [148.1091618276]</option> + <option value="139">139: mTRAQ of K 13C(3) 15N [144.1020624208]</option> + <option value="140">140: mTRAQ of K light [140.094963014]</option> + <option value="141">141: mTRAQ of peptide N-term 13C(3) 15N [144.1020624208]</option> + <option value="142">142: mTRAQ of peptide N-term 13C(6) 15N(2) [148.1091618276]</option> + <option value="143">143: mTRAQ of peptide N-term light [140.094963014]</option> + <option value="144">144: Nethylmaleimide of C [125.04767846841]</option> + <option value="145">145: NIPCAM of C [99.06841391299]</option> + <option value="146">146: Nitrosylation of C [28.99016359229]</option> + <option value="147">147: Nitrosylation of Y [44.985078211849995]</option> + <option value="148">148: Oxidation of C [15.99491461956]</option> + <option value="149">149: Oxidation of K [15.99491461956]</option> + <option value="150">150: Oxidation of N [15.99491461956]</option> + <option value="151">151: Oxidation of P [15.99491461956]</option> + <option value="152">152: Oxidation to Kynurenine of W [3.9949146195599994]</option> + <option value="153">153: Palmitoylation of C [238.22966558166]</option> + <option value="154">154: Palmitoylation of K [238.22966558166]</option> + <option value="155">155: Palmitoylation of protein N-term [238.22966558166]</option> + <option value="156">156: Palmitoylation of S [238.22966558166]</option> + <option value="157">157: Palmitoylation of T [238.22966558166]</option> + <option value="158">158: Potassium on D [37.95588145493]</option> + <option value="159">159: Potassium on E [37.95588145493]</option> + <option value="160">160: Proline 13C(5) [5.016774189000003]</option> + <option value="161">161: Propionamide of C [71.03711378471]</option> + <option value="162">162: Propionamide of K [71.03711378471]</option> + <option value="163">163: Propionamide of peptide N-term [71.03711378471]</option> + <option value="164">164: Propionyl of K heavy [59.03627926124]</option> + <option value="165">165: Propionyl of K light [56.02621474784]</option> + <option value="166">166: Propionyl of peptide N-term heavy [59.03627926124]</option> + <option value="167">167: Propionyl of peptide N-term light [56.02621474784]</option> + <option value="168">168: Pyridoxal phosphate of K [229.01400898916]</option> + <option value="169">169: Pyridylethyl of C [105.05784922929]</option> + <option value="170">170: Pyrolidone from carbamidomethylated C [-17.02654910101]</option> + <option value="171">171: Quinone of W [29.974179174979998]</option> + <option value="172">172: Quinone of Y [29.974179174979998]</option> + <option value="173">173: S-nitrosylation [28.99016359229]</option> + <option value="174">174: Sodium adduct to D [21.98194424883]</option> + <option value="175">175: Sodium adduct to E [21.98194424883]</option> + <option value="176">176: Succinylation of K [100.01604398696]</option> + <option value="177">177: Sulfation of S [79.95681485867999]</option> + <option value="178">178: Sulfation of T [79.95681485867999]</option> + <option value="179">179: Sulfation of Y [79.95681485867999]</option> + <option value="180">180: SUMO-2/3 Q87R [471.20776092011) -</option> + <option value="181">181: Thioacyl of peptide N-term [87.99828574784]</option> + <option value="182">182: TMT 10-plex of K+4 [233.18803911764) -</option> + <option value="183">183: TMT 10-plex of K+6 [235.18306116152) -</option> + <option value="184">184: TMT 10-plex of K+8 [237.17713094832) -</option> + <option value="185">185: TMT 11-plex of K+4 [233.18803911764) -</option> + <option value="186">186: TMT 11-plex of K+6 [235.18306116152) -</option> + <option value="187">187: TMT 11-plex of K+8 [237.17713094832) -</option> + <option value="188">188: TMT 6-plex of K+4 [233.18803911764) -</option> + <option value="189">189: TMT 6-plex of K+6 [235.18306116152) -</option> + <option value="190">190: TMT 6-plex of K+8 [237.17713094832) -</option> + <option value="191">191: Trideuterated Methyl Ester of D [17.034480301330003]</option> + <option value="192">192: Trideuterated Methyl Ester of E [17.034480301330003]</option> + <option value="193">193: Trideuterated Methyl Ester of K [17.034480301330003]</option> + <option value="194">194: Trideuterated Methyl Ester of peptide C-term [17.034480301330003]</option> + <option value="195">195: Trideuterated Methyl Ester of R [17.034480301330003]</option> + <option value="196">196: Trimethylation of K [42.04695019242]</option> + <option value="197">197: Trimethylation of protein N-term A [42.04695019242]</option> + <option value="198">198: Trimethylation of R [42.04695019242]</option> + <option value="199">199: Trioxidation of C [47.98474385868]</option> + <option value="200">200: Zinc on D [61.913492135860004]</option> + <option value="201">201: Zinc on E [61.913492135860004]</option> + <option value="202">202: 15N-oxobutanoic of C [-18.023584]</option> + <option value="203">203: 15N-oxobutanoic of protein S [-18.023584]</option> + <option value="204">204: 15N-oxobutanoic of protein T [-18.023584]</option> + <option value="205">205: 2-dimethylsuccinyl of C [144.042259]</option> + <option value="206">206: 2-monomethylsuccinyl of C [130.026609]</option> + <option value="207">207: 2-nitrobenzyl of Y [135.032028]</option> + <option value="208">208: 2-succinyl of C [116.010959]</option> + <option value="209">209: 3-deoxyglucosone of R [144.042259]</option> + <option value="210">210: 3-phosphoglyceryl of K [167.982375]</option> + <option value="211">211: 3sulfo of N-term [183.983029]</option> + <option value="212">212: 4-ONE of C [154.09938]</option> + <option value="213">213: 4-ONE of H [154.09938]</option> + <option value="214">214: 4-ONE of K [154.09938]</option> + <option value="215">215: 4-ONE+Delta:H(-2)O(-1) of C [136.088815]</option> + <option value="216">216: 4-ONE+Delta:H(-2)O(-1) of H [136.088815]</option> + <option value="217">217: 4-ONE+Delta:H(-2)O(-1) of K [136.088815]</option> + <option value="218">218: a-type-ion of C-term [-46.005479]</option> + <option value="219">219: AccQTag of K [170.048013]</option> + <option value="220">220: AccQTag of N-term [170.048013]</option> + <option value="221">221: Acetyl of C [42.010565]</option> + <option value="222">222: Acetyl of H [42.010565]</option> + <option value="223">223: Acetyl of K [42.010565]</option> + <option value="224">224: Acetyl of N-term [42.010565]</option> + <option value="225">225: Acetyl of protein N-term [42.010565]</option> + <option value="226">226: Acetyl of S [42.010565]</option> + <option value="227">227: Acetyl of T [42.010565]</option> + <option value="228">228: Acetyl of Y [42.010565]</option> + <option value="229">229: Acetyl:13C(2) of K [44.017274]</option> + <option value="230">230: Acetyl:13C(2) of protein N-term [44.017274]</option> + <option value="231">231: Acetyl:2H(3) of H [45.029395]</option> + <option value="232">232: Acetyl:2H(3) of K [45.029395]</option> + <option value="233">233: Acetyl:2H(3) of N-term [45.029395]</option> + <option value="234">234: Acetyl:2H(3) of protein N-term [45.029395]</option> + <option value="235">235: Acetyl:2H(3) of S [45.029395]</option> + <option value="236">236: Acetyl:2H(3) of T [45.029395]</option> + <option value="237">237: Acetyl:2H(3) of Y [45.029395]</option> + <option value="238">238: Acetyldeoxyhypusine of K [97.089149]</option> + <option value="239">239: Acetylhypusine of K [113.084064]</option> + <option value="240">240: AEBS of H [183.035399]</option> + <option value="241">241: AEBS of K [183.035399]</option> + <option value="242">242: AEBS of protein N-term [183.035399]</option> + <option value="243">243: AEBS of S [183.035399]</option> + <option value="244">244: AEBS of Y [183.035399]</option> + <option value="245">245: AEC-MAEC of S [59.019355]</option> + <option value="246">246: AEC-MAEC of T [59.019355]</option> + <option value="247">247: AEC-MAEC:2H(4) of S [63.044462]</option> + <option value="248">248: AEC-MAEC:2H(4) of T [63.044462]</option> + <option value="249">249: AHA-Alkyne of M [107.077339]</option> + <option value="250">250: AHA-SS of M [195.075625]</option> + <option value="251">251: Amidated of C-term [-0.984016]</option> + <option value="252">252: Amidated of protein C-term [-0.984016]</option> + <option value="253">253: Amidine of K [41.026549]</option> + <option value="254">254: Amidine of N-term [41.026549]</option> + <option value="255">255: Amidino of C [42.021798]</option> + <option value="256">256: Amino of Y [15.010899]</option> + <option value="257">257: Ammonia-loss of C [-17.026549]</option> + <option value="258">258: Ammonia-loss of N [-17.026549]</option> + <option value="259">259: Ammonia-loss of protein S [-17.026549]</option> + <option value="260">260: Ammonia-loss of protein T [-17.026549]</option> + <option value="261">261: Ammonium of C-term [17.026549]</option> + <option value="262">262: Ammonium of D [17.026549]</option> + <option value="263">263: Ammonium of E [17.026549]</option> + <option value="264">264: Arg of N-term [156.101111]</option> + <option value="265">265: Arg->GluSA of R [-43.053433]</option> + <option value="266">266: Arg->Npo of R [80.985078]</option> + <option value="267">267: Arg->Orn of R [-42.021798]</option> + <option value="268">268: Arg-loss of R [-156.101111]</option> + <option value="269">269: Argbiotinhydrazide of R [199.066699]</option> + <option value="270">270: AzidoF of F [41.001397]</option> + <option value="271">271: azole of C [-20.026215]</option> + <option value="272">272: azole of S [-20.026215]</option> + <option value="273">273: Bacillosamine of N [228.111007]</option> + <option value="274">274: Benzoyl of K [104.026215]</option> + <option value="275">275: Benzoyl of N-term [104.026215]</option> + <option value="276">276: benzylguanidine of K [132.068748]</option> + <option value="277">277: BHT of C [218.167065]</option> + <option value="278">278: BHT of H [218.167065]</option> + <option value="279">279: BHT of K [218.167065]</option> + <option value="280">280: BHTOH of C [234.16198]</option> + <option value="281">281: BHTOH of H [234.16198]</option> + <option value="282">282: BHTOH of K [234.16198]</option> + <option value="283">283: Biotin of K [226.077598]</option> + <option value="284">284: Biotin of N-term [226.077598]</option> + <option value="285">285: Biotin:Thermo-88310 of K [196.121178]</option> + <option value="286">286: BITC of C [149.02992]</option> + <option value="287">287: BITC of K [149.02992]</option> + <option value="288">288: BITC of N-term [149.02992]</option> + <option value="289">289: Brij35 of N-term [168.187801]</option> + <option value="290">290: Brij58 of N-term [224.250401]</option> + <option value="291">291: Bromo of F [77.910511]</option> + <option value="292">292: Bromo of H [77.910511]</option> + <option value="293">293: Bromo of W [77.910511]</option> + <option value="294">294: Bromo of Y [77.910511]</option> + <option value="295">295: Bromobimane of C [190.074228]</option> + <option value="296">296: Butyryl of K [70.041865]</option> + <option value="297">297: C8-QAT of K [227.224915]</option> + <option value="298">298: C8-QAT of N-term [227.224915]</option> + <option value="299">299: CAF of N-term [135.983029]</option> + <option value="300">300: CAMthiopropanoyl of K [145.019749]</option> + <option value="301">301: CAMthiopropanoyl of protein N-term [145.019749]</option> + <option value="302">302: Carbamidomethyl of C [57.021464]</option> + <option value="303">303: Carbamidomethyl of D [57.021464]</option> + <option value="304">304: Carbamidomethyl of E [57.021464]</option> + <option value="305">305: Carbamidomethyl of H [57.021464]</option> + <option value="306">306: Carbamidomethyl of K [57.021464]</option> + <option value="307">307: Carbamidomethyl of N-term [57.021464]</option> + <option value="308">308: Carbamidomethyl of S [57.021464]</option> + <option value="309">309: Carbamidomethyl of T [57.021464]</option> + <option value="310">310: Carbamidomethyl of U [57.021464]</option> + <option value="311">311: Carbamidomethyl of Y [57.021464]</option> + <option value="312">312: CarbamidomethylDTT of C [209.018035]</option> + <option value="313">313: Carbamyl of C [43.005814]</option> + <option value="314">314: Carbamyl of K [43.005814]</option> + <option value="315">315: Carbamyl of M [43.005814]</option> + <option value="316">316: Carbamyl of N-term [43.005814]</option> + <option value="317">317: Carbamyl of protein N-term [43.005814]</option> + <option value="318">318: Carbamyl of R [43.005814]</option> + <option value="319">319: Carbamyl of S [43.005814]</option> + <option value="320">320: Carbamyl of T [43.005814]</option> + <option value="321">321: Carbamyl of Y [43.005814]</option> + <option value="322">322: Carbofuran of S [58.029289]</option> + <option value="323">323: Carboxy of D [43.989829]</option> + <option value="324">324: Carboxy of E [43.989829]</option> + <option value="325">325: Carboxy of K [43.989829]</option> + <option value="326">326: Carboxy of protein M [43.989829]</option> + <option value="327">327: Carboxy of W [43.989829]</option> + <option value="328">328: Carboxy->Thiocarboxy of protein G [15.977156]</option> + <option value="329">329: Carboxyethyl of H [72.021129]</option> + <option value="330">330: Carboxyethyl of K [72.021129]</option> + <option value="331">331: Carboxyethylpyrrole of K [122.036779]</option> + <option value="332">332: Carboxymethyl of C [58.005479]</option> + <option value="333">333: Carboxymethyl of K [58.005479]</option> + <option value="334">334: Carboxymethyl of N-term [58.005479]</option> + <option value="335">335: Carboxymethyl of U [58.005479]</option> + <option value="336">336: Carboxymethyl of W [58.005479]</option> + <option value="337">337: Carboxymethyl:13C(2) of C [60.012189]</option> + <option value="338">338: CarboxymethylDMAP of N-term [162.079313]</option> + <option value="339">339: CarboxymethylDTT of C [210.00205]</option> + <option value="340">340: Cation:Ag of C-term [105.897267]</option> + <option value="341">341: Cation:Ag of D [105.897267]</option> + <option value="342">342: Cation:Ag of E [105.897267]</option> + <option value="343">343: Cation:Ca[II] of C-term [37.946941]</option> + <option value="344">344: Cation:Ca[II] of D [37.946941]</option> + <option value="345">345: Cation:Ca[II] of E [37.946941]</option> + <option value="346">346: Cation:Cu[I] of C-term [61.921774]</option> + <option value="347">347: Cation:Cu[I] of D [61.921774]</option> + <option value="348">348: Cation:Cu[I] of E [61.921774]</option> + <option value="349">349: Cation:Cu[I] of H [61.921774]</option> + <option value="350">350: Cation:Fe[II] of C-term [53.919289]</option> + <option value="351">351: Cation:Fe[II] of D [53.919289]</option> + <option value="352">352: Cation:Fe[II] of E [53.919289]</option> + <option value="353">353: Cation:K of C-term [37.955882]</option> + <option value="354">354: Cation:K of D [37.955882]</option> + <option value="355">355: Cation:K of E [37.955882]</option> + <option value="356">356: Cation:Li of C-term [6.008178]</option> + <option value="357">357: Cation:Li of D [6.008178]</option> + <option value="358">358: Cation:Li of E [6.008178]</option> + <option value="359">359: Cation:Mg[II] of C-term [21.969392]</option> + <option value="360">360: Cation:Mg[II] of D [21.969392]</option> + <option value="361">361: Cation:Mg[II] of E [21.969392]</option> + <option value="362">362: Cation:Na of C-term [21.981943]</option> + <option value="363">363: Cation:Na of D [21.981943]</option> + <option value="364">364: Cation:Na of E [21.981943]</option> + <option value="365">365: Cation:Ni[II] of C-term [55.919696]</option> + <option value="366">366: Cation:Ni[II] of D [55.919696]</option> + <option value="367">367: Cation:Ni[II] of E [55.919696]</option> + <option value="368">368: Cation:Zn[II] of C-term [61.913495]</option> + <option value="369">369: Cation:Zn[II] of D [61.913495]</option> + <option value="370">370: Cation:Zn[II] of E [61.913495]</option> + <option value="371">371: Cation:Zn[II] of H [61.913495]</option> + <option value="372">372: cGMP+RMP-loss of C [150.041585]</option> + <option value="373">373: cGMP+RMP-loss of S [150.041585]</option> + <option value="374">374: Chlorination of Y [33.961028]</option> + <option value="375">375: Chlorpyrifos of S [153.013912]</option> + <option value="376">376: Chlorpyrifos of T [153.013912]</option> + <option value="377">377: Chlorpyrifos of Y [153.013912]</option> + <option value="378">378: CLIP_TRAQ_2 of K [141.098318]</option> + <option value="379">379: CLIP_TRAQ_2 of N-term [141.098318]</option> + <option value="380">380: CLIP_TRAQ_2 of Y [141.098318]</option> + <option value="381">381: CLIP_TRAQ_4 of K [244.101452]</option> + <option value="382">382: CLIP_TRAQ_4 of N-term [244.101452]</option> + <option value="383">383: CLIP_TRAQ_4 of Y [244.101452]</option> + <option value="384">384: Cresylphosphate of H [170.013281]</option> + <option value="385">385: Cresylphosphate of K [170.013281]</option> + <option value="386">386: Cresylphosphate of R [170.013281]</option> + <option value="387">387: Cresylphosphate of S [170.013281]</option> + <option value="388">388: Cresylphosphate of T [170.013281]</option> + <option value="389">389: Cresylphosphate of Y [170.013281]</option> + <option value="390">390: Crotonaldehyde of C [70.041865]</option> + <option value="391">391: Crotonaldehyde of H [70.041865]</option> + <option value="392">392: Crotonaldehyde of K [70.041865]</option> + <option value="393">393: Crotonyl of K [68.026215]</option> + <option value="394">394: Cyano of C [24.995249]</option> + <option value="395">395: Cys->CamSec of C [104.965913]</option> + <option value="396">396: Cys->Dha of C [-33.987721]</option> + <option value="397">397: Cys->ethylaminoAla of C [11.070128]</option> + <option value="398">398: Cys->methylaminoAla of C [-2.945522]</option> + <option value="399">399: Cys->Oxoalanine of C [-17.992806]</option> + <option value="400">400: Cys->PyruvicAcid of protein C [-33.003705]</option> + <option value="401">401: Cys->SecNEM of C [172.992127]</option> + <option value="402">402: Cys->SecNEM:2H(5) of C [178.023511]</option> + <option value="403">403: Cysteinyl of C [119.004099]</option> + <option value="404">404: DAET of S [87.050655]</option> + <option value="405">405: DAET of T [87.050655]</option> + <option value="406">406: Dansyl of K [233.051049]</option> + <option value="407">407: Dansyl of N-term [233.051049]</option> + <option value="408">408: Deamidated of N [0.984016]</option> + <option value="409">409: Deamidated of protein F [0.984016]</option> + <option value="410">410: Deamidated of Q [0.984016]</option> + <option value="411">411: Deamidated of R [0.984016]</option> + <option value="412">412: Deamidated:18O(1) of N [2.988261]</option> + <option value="413">413: Deamidated:18O(1) of Q [2.988261]</option> + <option value="414">414: Decanoyl of S [154.135765]</option> + <option value="415">415: Decanoyl of T [154.135765]</option> + <option value="416">416: Dehydrated of C [-18.010565]</option> + <option value="417">417: Dehydrated of D [-18.010565]</option> + <option value="418">418: Dehydrated of protein N [-18.010565]</option> + <option value="419">419: Dehydrated of protein Q [-18.010565]</option> + <option value="420">420: Dehydrated of S [-18.010565]</option> + <option value="421">421: Dehydrated of T [-18.010565]</option> + <option value="422">422: Dehydrated of Y [-18.010565]</option> + <option value="423">423: Dehydro of C [-1.007825]</option> + <option value="424">424: Delta:H(1)N(-1)18O(1) of N [2.988261]</option> + <option value="425">425: Delta:H(2)C(2) of H [26.01565]</option> + <option value="426">426: Delta:H(2)C(2) of K [26.01565]</option> + <option value="427">427: Delta:H(2)C(2) of N-term [26.01565]</option> + <option value="428">428: Delta:H(2)C(2) of protein N-term [26.01565]</option> + <option value="429">429: Delta:H(2)C(3) of K [38.01565]</option> + <option value="430">430: Delta:H(2)C(3)O(1) of K [54.010565]</option> + <option value="431">431: Delta:H(2)C(3)O(1) of R [54.010565]</option> + <option value="432">432: Delta:H(2)C(5) of K [62.01565]</option> + <option value="433">433: Delta:H(4)C(2) of H [28.0313]</option> + <option value="434">434: Delta:H(4)C(2) of K [28.0313]</option> + <option value="435">435: Delta:H(4)C(2) of N-term [28.0313]</option> + <option value="436">436: Delta:H(4)C(2)O(-1)S(1) of S [44.008456]</option> + <option value="437">437: Delta:H(4)C(3) of H [40.0313]</option> + <option value="438">438: Delta:H(4)C(3) of K [40.0313]</option> + <option value="439">439: Delta:H(4)C(3) of protein N-term [40.0313]</option> + <option value="440">440: Delta:H(4)C(3)O(1) of C [56.026215]</option> + <option value="441">441: Delta:H(4)C(3)O(1) of H [56.026215]</option> + <option value="442">442: Delta:H(4)C(3)O(1) of K [56.026215]</option> + <option value="443">443: Delta:H(4)C(6) of K [76.0313]</option> + <option value="444">444: Delta:H(5)C(2) of P [29.039125]</option> + <option value="445">445: Delta:H(6)C(3)O(1) of C [58.041865]</option> + <option value="446">446: Delta:H(6)C(3)O(1) of H [58.041865]</option> + <option value="447">447: Delta:H(6)C(3)O(1) of K [58.041865]</option> + <option value="448">448: Delta:H(6)C(3)O(1) of protein N-term [58.041865]</option> + <option value="449">449: Delta:H(6)C(6)O(1) of K [94.041865]</option> + <option value="450">450: Delta:H(8)C(6)O(1) of K [96.057515]</option> + <option value="451">451: Delta:H(8)C(6)O(1) of protein N-term [96.057515]</option> + <option value="452">452: Delta:H(8)C(6)O(2) of K [112.05243]</option> + <option value="453">453: Delta:Hg(1) of C [201.970617]</option> + <option value="454">454: Delta:S(-1)Se(1) of C [47.944449]</option> + <option value="455">455: Delta:S(-1)Se(1) of M [47.944449]</option> + <option value="456">456: Delta:Se(1) of C [79.91652]</option> + <option value="457">457: Deoxy of D [-15.994915]</option> + <option value="458">458: Deoxy of S [-15.994915]</option> + <option value="459">459: Deoxy of T [-15.994915]</option> + <option value="460">460: Deoxyhypusine of K [71.073499]</option> + <option value="461">461: Deoxyhypusine of Q [71.073499]</option> + <option value="462">462: DeStreak of C [75.998285]</option> + <option value="463">463: Dethiomethyl of M [-48.003371]</option> + <option value="464">464: dHex of N [146.057909]</option> + <option value="465">465: dHex of S [146.057909]</option> + <option value="466">466: dHex of T [146.057909]</option> + <option value="467">467: DHP of C [118.065674]</option> + <option value="468">468: DiART6plex of K [217.162932]</option> + <option value="469">469: DiART6plex of N-term [217.162932]</option> + <option value="470">470: DiART6plex of protein N-term [217.162932]</option> + <option value="471">471: DiART6plex of Y [217.162932]</option> + <option value="472">472: DiART6plex115 of K [217.156612]</option> + <option value="473">473: DiART6plex115 of N-term [217.156612]</option> + <option value="474">474: DiART6plex115 of protein N-term [217.156612]</option> + <option value="475">475: DiART6plex115 of Y [217.156612]</option> + <option value="476">476: DiART6plex116/119 of K [217.168776]</option> + <option value="477">477: DiART6plex116/119 of N-term [217.168776]</option> + <option value="478">478: DiART6plex116/119 of protein N-term [217.168776]</option> + <option value="479">479: DiART6plex116/119 of Y [217.168776]</option> + <option value="480">480: DiART6plex117 of K [217.162456]</option> + <option value="481">481: DiART6plex117 of N-term [217.162456]</option> + <option value="482">482: DiART6plex117 of protein N-term [217.162456]</option> + <option value="483">483: DiART6plex117 of Y [217.162456]</option> + <option value="484">484: DiART6plex118 of K [217.175096]</option> + <option value="485">485: DiART6plex118 of N-term [217.175096]</option> + <option value="486">486: DiART6plex118 of protein N-term [217.175096]</option> + <option value="487">487: DiART6plex118 of Y [217.175096]</option> + <option value="488">488: Dibromo of Y [155.821022]</option> + <option value="489">489: Dicarbamidomethyl of C [114.042927]</option> + <option value="490">490: Dicarbamidomethyl of H [114.042927]</option> + <option value="491">491: Dicarbamidomethyl of K [114.042927]</option> + <option value="492">492: Dicarbamidomethyl of N-term [114.042927]</option> + <option value="493">493: Dicarbamidomethyl of R [114.042927]</option> + <option value="494">494: dichlorination of C [67.922055]</option> + <option value="495">495: dichlorination of Y [67.922055]</option> + <option value="496">496: Didehydro of K [-2.01565]</option> + <option value="497">497: Didehydro of S [-2.01565]</option> + <option value="498">498: Diethyl of K [56.0626]</option> + <option value="499">499: Diethyl of N-term [56.0626]</option> + <option value="500">500: Diethylphosphate of C [136.028931]</option> + <option value="501">501: Diethylphosphate of H [136.028931]</option> + <option value="502">502: Diethylphosphate of K [136.028931]</option> + <option value="503">503: Diethylphosphate of N-term [136.028931]</option> + <option value="504">504: Diethylphosphate of S [136.028931]</option> + <option value="505">505: Diethylphosphate of T [136.028931]</option> + <option value="506">506: Diethylphosphate of Y [136.028931]</option> + <option value="507">507: Difuran of Y [132.021129]</option> + <option value="508">508: Dihydroxyimidazolidine of R [72.021129]</option> + <option value="509">509: Diisopropylphosphate of K [164.060231]</option> + <option value="510">510: Diisopropylphosphate of N-term [164.060231]</option> + <option value="511">511: Diisopropylphosphate of S [164.060231]</option> + <option value="512">512: Diisopropylphosphate of T [164.060231]</option> + <option value="513">513: Diisopropylphosphate of Y [164.060231]</option> + <option value="514">514: DiLeu4plex of K [145.132163]</option> + <option value="515">515: DiLeu4plex of N-term [145.132163]</option> + <option value="516">516: DiLeu4plex of Y [145.132163]</option> + <option value="517">517: DiLeu4plex115 of K [145.12]</option> + <option value="518">518: DiLeu4plex115 of N-term [145.12]</option> + <option value="519">519: DiLeu4plex115 of Y [145.12]</option> + <option value="520">520: DiLeu4plex117 of K [145.128307]</option> + <option value="521">521: DiLeu4plex117 of N-term [145.128307]</option> + <option value="522">522: DiLeu4plex117 of Y [145.128307]</option> + <option value="523">523: DiLeu4plex118 of K [145.140471]</option> + <option value="524">524: DiLeu4plex118 of N-term [145.140471]</option> + <option value="525">525: DiLeu4plex118 of Y [145.140471]</option> + <option value="526">526: Dimethyl of K [28.0313]</option> + <option value="527">527: Dimethyl of N [28.0313]</option> + <option value="528">528: Dimethyl of N-term [28.0313]</option> + <option value="529">529: Dimethyl of protein N-term [28.0313]</option> + <option value="530">530: Dimethyl of protein P [28.0313]</option> + <option value="531">531: Dimethyl of R [28.0313]</option> + <option value="532">532: Dimethyl:2H(4) of K [32.056407]</option> + <option value="533">533: Dimethyl:2H(4) of N-term [32.056407]</option> + <option value="534">534: Dimethyl:2H(4) of protein N-term [32.056407]</option> + <option value="535">535: Dimethyl:2H(4) of R [32.056407]</option> + <option value="536">536: Dimethyl:2H(4)13C(2) of K [34.063117]</option> + <option value="537">537: Dimethyl:2H(4)13C(2) of N-term [34.063117]</option> + <option value="538">538: Dimethyl:2H(4)13C(2) of protein N-term [34.063117]</option> + <option value="539">539: Dimethyl:2H(4)13C(2) of R [34.063117]</option> + <option value="540">540: Dimethyl:2H(6) of K [34.068961]</option> + <option value="541">541: Dimethyl:2H(6) of N-term [34.068961]</option> + <option value="542">542: Dimethyl:2H(6) of R [34.068961]</option> + <option value="543">543: Dimethyl:2H(6)13C(2) of K [36.07567]</option> + <option value="544">544: Dimethyl:2H(6)13C(2) of N-term [36.07567]</option> + <option value="545">545: Dimethyl:2H(6)13C(2) of protein N-term [36.07567]</option> + <option value="546">546: Dimethyl:2H(6)13C(2) of R [36.07567]</option> + <option value="547">547: Dimethylaminoethyl of C [71.073499]</option> + <option value="548">548: DimethylArsino of C [103.960719]</option> + <option value="549">549: DimethylpyrroleAdduct of K [78.04695]</option> + <option value="550">550: Dioxidation of C [31.989829]</option> + <option value="551">551: Dioxidation of F [31.989829]</option> + <option value="552">552: Dioxidation of K [31.989829]</option> + <option value="553">553: Dioxidation of P [31.989829]</option> + <option value="554">554: Dioxidation of R [31.989829]</option> + <option value="555">555: Dioxidation of U [31.989829]</option> + <option value="556">556: Dioxidation of Y [31.989829]</option> + <option value="557">557: Diphthamide of H [142.110613]</option> + <option value="558">558: Dipyridyl of C [225.090212]</option> + <option value="559">559: DMPO of C [111.068414]</option> + <option value="560">560: DMPO of H [111.068414]</option> + <option value="561">561: DMPO of Y [111.068414]</option> + <option value="562">562: DNCB_hapten of C [166.001457]</option> + <option value="563">563: DNCB_hapten of H [166.001457]</option> + <option value="564">564: DNCB_hapten of K [166.001457]</option> + <option value="565">565: DNCB_hapten of Y [166.001457]</option> + <option value="566">566: dNIC of K [109.048119]</option> + <option value="567">567: dNIC of N-term [109.048119]</option> + <option value="568">568: DNPS of C [198.981352]</option> + <option value="569">569: DNPS of W [198.981352]</option> + <option value="570">570: DTT_C of C [120.0245]</option> + <option value="571">571: DTT_C:2H(6) of C [126.062161]</option> + <option value="572">572: DTT_ST of S [136.001656]</option> + <option value="573">573: DTT_ST of T [136.001656]</option> + <option value="574">574: DTT_ST:2H(6) of S [142.039317]</option> + <option value="575">575: DTT_ST:2H(6) of T [142.039317]</option> + <option value="576">576: EQAT of C [184.157563]</option> + <option value="577">577: EQAT:2H(5) of C [189.188947]</option> + <option value="578">578: Ethanedithiol of S [75.980527]</option> + <option value="579">579: Ethanedithiol of T [75.980527]</option> + <option value="580">580: Ethanolamine of C [43.042199]</option> + <option value="581">581: Ethanolamine of C-term [43.042199]</option> + <option value="582">582: Ethanolamine of D [43.042199]</option> + <option value="583">583: Ethanolamine of E [43.042199]</option> + <option value="584">584: Ethanolyl of C [44.026215]</option> + <option value="585">585: Ethanolyl of K [44.026215]</option> + <option value="586">586: Ethanolyl of R [44.026215]</option> + <option value="587">587: Ethoxyformyl of H [72.021129]</option> + <option value="588">588: Ethyl of C-term [28.0313]</option> + <option value="589">589: Ethyl of D [28.0313]</option> + <option value="590">590: Ethyl of E [28.0313]</option> + <option value="591">591: Ethyl of K [28.0313]</option> + <option value="592">592: Ethyl of N-term [28.0313]</option> + <option value="593">593: Ethyl of protein N-term [28.0313]</option> + <option value="594">594: Ethyl+Deamidated of N [29.015316]</option> + <option value="595">595: Ethyl+Deamidated of Q [29.015316]</option> + <option value="596">596: ethylamino of S [27.047285]</option> + <option value="597">597: ethylamino of T [27.047285]</option> + <option value="598">598: Ethylphosphate of K [107.997631]</option> + <option value="599">599: Ethylphosphate of N-term [107.997631]</option> + <option value="600">600: Ethylphosphate of S [107.997631]</option> + <option value="601">601: Ethylphosphate of T [107.997631]</option> + <option value="602">602: Ethylphosphate of Y [107.997631]</option> + <option value="603">603: ethylsulfonylethyl of C [120.0245]</option> + <option value="604">604: ethylsulfonylethyl of H [120.0245]</option> + <option value="605">605: ethylsulfonylethyl of K [120.0245]</option> + <option value="606">606: Farnesyl of C [204.187801]</option> + <option value="607">607: Fluoro of A [17.990578]</option> + <option value="608">608: Fluoro of F [17.990578]</option> + <option value="609">609: Fluoro of W [17.990578]</option> + <option value="610">610: Fluoro of Y [17.990578]</option> + <option value="611">611: Formyl of K [27.994915]</option> + <option value="612">612: Formyl of N-term [27.994915]</option> + <option value="613">613: Formyl of protein N-term [27.994915]</option> + <option value="614">614: Formyl of S [27.994915]</option> + <option value="615">615: Formyl of T [27.994915]</option> + <option value="616">616: Furan of Y [66.010565]</option> + <option value="617">617: G-H1 of R [39.994915]</option> + <option value="618">618: Galactosyl of K [178.047738]</option> + <option value="619">619: Galactosyl of N-term [178.047738]</option> + <option value="620">620: GEE of Q [86.036779]</option> + <option value="621">621: GG of C [114.042927]</option> + <option value="622">622: GG of K [114.042927]</option> + <option value="623">623: GG of protein N-term [114.042927]</option> + <option value="624">624: GG of S [114.042927]</option> + <option value="625">625: GG of T [114.042927]</option> + <option value="626">626: GGQ of K [242.101505]</option> + <option value="627">627: GIST-Quat of K [127.099714]</option> + <option value="628">628: GIST-Quat of N-term [127.099714]</option> + <option value="629">629: GIST-Quat:2H(3) of K [130.118544]</option> + <option value="630">630: GIST-Quat:2H(3) of N-term [130.118544]</option> + <option value="631">631: GIST-Quat:2H(6) of K [133.137375]</option> + <option value="632">632: GIST-Quat:2H(6) of N-term [133.137375]</option> + <option value="633">633: GIST-Quat:2H(9) of K [136.156205]</option> + <option value="634">634: GIST-Quat:2H(9) of N-term [136.156205]</option> + <option value="635">635: Gln->pyro-Glu of Q [-17.026549]</option> + <option value="636">636: Glu of E [129.042593]</option> + <option value="637">637: Glu of protein C-term [129.042593]</option> + <option value="638">638: Glu->pyro-Glu of E [-18.010565]</option> + <option value="639">639: Glu->pyro-Glu+Methyl of E [-3.994915]</option> + <option value="640">640: Glu->pyro-Glu+Methyl:2H(2)13C(1) of E [-0.979006]</option> + <option value="641">641: glucosone of R [160.037173]</option> + <option value="642">642: Glucuronyl of protein N-term [176.032088]</option> + <option value="643">643: Glucuronyl of S [176.032088]</option> + <option value="644">644: Glucuronyl of T [176.032088]</option> + <option value="645">645: Gly of K [57.021464]</option> + <option value="646">646: Gly of S [57.021464]</option> + <option value="647">647: Gly of T [57.021464]</option> + <option value="648">648: Gly-loss+Amide of G [-58.005479]</option> + <option value="649">649: Glycerophospho of S [154.00311]</option> + <option value="650">650: GlycerylPE of E [197.04531]</option> + <option value="651">651: glycidamide of K [87.032028]</option> + <option value="652">652: glycidamide of N-term [87.032028]</option> + <option value="653">653: Glycosyl of P [148.037173]</option> + <option value="654">654: GPIanchor of protein C-term [123.00853]</option> + <option value="655">655: Guanidinyl of K [42.021798]</option> + <option value="656">656: Guanidinyl of N-term [42.021798]</option> + <option value="657">657: HCysteinyl of C [133.019749]</option> + <option value="658">658: HCysThiolactone of K [117.024835]</option> + <option value="659">659: Hep of K [192.063388]</option> + <option value="660">660: Hep of N [192.063388]</option> + <option value="661">661: Hep of Q [192.063388]</option> + <option value="662">662: Hep of R [192.063388]</option> + <option value="663">663: Hep of S [192.063388]</option> + <option value="664">664: Hep of T [192.063388]</option> + <option value="665">665: Hex of C [162.052824]</option> + <option value="666">666: Hex of K [162.052824]</option> + <option value="667">667: Hex of N [162.052824]</option> + <option value="668">668: Hex of N-term [162.052824]</option> + <option value="669">669: Hex of R [162.052824]</option> + <option value="670">670: Hex of S [162.052824]</option> + <option value="671">671: Hex of T [162.052824]</option> + <option value="672">672: Hex of W [162.052824]</option> + <option value="673">673: Hex of Y [162.052824]</option> + <option value="674">674: HexN of K [161.068808]</option> + <option value="675">675: HexN of N [161.068808]</option> + <option value="676">676: HexN of S [161.068808]</option> + <option value="677">677: HexN of T [161.068808]</option> + <option value="678">678: HexN of W [161.068808]</option> + <option value="679">679: HexNAc of N [203.079373]</option> + <option value="680">680: HMVK of C [86.036779]</option> + <option value="681">681: HN2_mustard of C [101.084064]</option> + <option value="682">682: HN2_mustard of H [101.084064]</option> + <option value="683">683: HN2_mustard of K [101.084064]</option> + <option value="684">684: HN3_mustard of C [131.094629]</option> + <option value="685">685: HN3_mustard of H [131.094629]</option> + <option value="686">686: HN3_mustard of K [131.094629]</option> + <option value="687">687: HNE of A [156.11503]</option> + <option value="688">688: HNE of C [156.11503]</option> + <option value="689">689: HNE of H [156.11503]</option> + <option value="690">690: HNE of K [156.11503]</option> + <option value="691">691: HNE of L [156.11503]</option> + <option value="692">692: HNE+Delta:H(2) of C [158.13068]</option> + <option value="693">693: HNE+Delta:H(2) of H [158.13068]</option> + <option value="694">694: HNE+Delta:H(2) of K [158.13068]</option> + <option value="695">695: HNE-Delta:H(2)O of C [138.104465]</option> + <option value="696">696: HNE-Delta:H(2)O of H [138.104465]</option> + <option value="697">697: HNE-Delta:H(2)O of K [138.104465]</option> + <option value="698">698: Homocysteic_acid of M [33.969094]</option> + <option value="699">699: HPG of R [132.021129]</option> + <option value="700">700: Hydroxamic_acid of D [15.010899]</option> + <option value="701">701: Hydroxamic_acid of E [15.010899]</option> + <option value="702">702: Hydroxycinnamyl of C [146.036779]</option> + <option value="703">703: Hydroxyfarnesyl of C [220.182715]</option> + <option value="704">704: Hydroxymethyl of N [30.010565]</option> + <option value="705">705: HydroxymethylOP of K [108.021129]</option> + <option value="706">706: Hydroxytrimethyl of K [59.04969]</option> + <option value="707">707: Hypusine of K [87.068414]</option> + <option value="708">708: ICAT-C of C [227.126991]</option> + <option value="709">709: ICAT-C:13C(9) of C [236.157185]</option> + <option value="710">710: ICDID of C [138.06808]</option> + <option value="711">711: ICDID:2H(6) of C [144.10574]</option> + <option value="712">712: ICPL of K [105.021464]</option> + <option value="713">713: ICPL of N-term [105.021464]</option> + <option value="714">714: ICPL of protein N-term [105.021464]</option> + <option value="715">715: ICPL:13C(6) of K [111.041593]</option> + <option value="716">716: ICPL:13C(6) of N-term [111.041593]</option> + <option value="717">717: ICPL:13C(6) of protein N-term [111.041593]</option> + <option value="718">718: ICPL:13C(6)2H(4) of K [115.0667]</option> + <option value="719">719: ICPL:13C(6)2H(4) of N-term [115.0667]</option> + <option value="720">720: ICPL:13C(6)2H(4) of protein N-term [115.0667]</option> + <option value="721">721: ICPL:2H(4) of K [109.046571]</option> + <option value="722">722: ICPL:2H(4) of N-term [109.046571]</option> + <option value="723">723: ICPL:2H(4) of protein N-term [109.046571]</option> + <option value="724">724: IDEnT of C [214.990469]</option> + <option value="725">725: IMID of K [68.037448]</option> + <option value="726">726: IMID:2H(4) of K [72.062555]</option> + <option value="727">727: Iminobiotin of K [225.093583]</option> + <option value="728">728: Iminobiotin of N-term [225.093583]</option> + <option value="729">729: Iodo of H [125.896648]</option> + <option value="730">730: Iodo of Y [125.896648]</option> + <option value="731">731: Iodoacetanilide of C [133.052764]</option> + <option value="732">732: Iodoacetanilide of K [133.052764]</option> + <option value="733">733: Iodoacetanilide of N-term [133.052764]</option> + <option value="734">734: Iodoacetanilide:13C(6) of C [139.072893]</option> + <option value="735">735: Iodoacetanilide:13C(6) of K [139.072893]</option> + <option value="736">736: Iodoacetanilide:13C(6) of N-term [139.072893]</option> + <option value="737">737: ISD_z+2_ion of N-term [-15.010899]</option> + <option value="738">738: Isopropylphospho of S [122.013281]</option> + <option value="739">739: Isopropylphospho of T [122.013281]</option> + <option value="740">740: Isopropylphospho of Y [122.013281]</option> + <option value="741">741: iTRAQ4plex of H [144.102063]</option> + <option value="742">742: iTRAQ4plex of K [144.102063]</option> + <option value="743">743: iTRAQ4plex of N-term [144.102063]</option> + <option value="744">744: iTRAQ4plex of protein N-term [144.102063]</option> + <option value="745">745: iTRAQ4plex of S [144.102063]</option> + <option value="746">746: iTRAQ4plex of T [144.102063]</option> + <option value="747">747: iTRAQ4plex of Y [144.102063]</option> + <option value="748">748: iTRAQ4plex114 of K [144.105918]</option> + <option value="749">749: iTRAQ4plex114 of N-term [144.105918]</option> + <option value="750">750: iTRAQ4plex114 of Y [144.105918]</option> + <option value="751">751: iTRAQ4plex115 of K [144.099599]</option> + <option value="752">752: iTRAQ4plex115 of N-term [144.099599]</option> + <option value="753">753: iTRAQ4plex115 of Y [144.099599]</option> + <option value="754">754: Label:13C(1)2H(3) of M [4.022185]</option> + <option value="755">755: Label:13C(1)2H(3)+Oxidation of M [20.0171]</option> + <option value="756">756: Label:13C(2)15N(2) of K [4.00078]</option> + <option value="757">757: Label:13C(3) of A [3.010064]</option> + <option value="758">758: Label:13C(3)15N(1) of A [4.007099]</option> + <option value="759">759: Label:13C(4) of M [4.013419]</option> + <option value="760">760: Label:13C(4)+Oxidation of M [20.008334]</option> + <option value="761">761: Label:13C(4)15N(1) of D [5.010454]</option> + <option value="762">762: Label:13C(4)15N(2)+GG of K [120.050417]</option> + <option value="763">763: Label:13C(5) of P [5.016774]</option> + <option value="764">764: Label:13C(5)15N(1) of E [6.013809]</option> + <option value="765">765: Label:13C(5)15N(1) of M [6.013809]</option> + <option value="766">766: Label:13C(5)15N(1) of P [6.013809]</option> + <option value="767">767: Label:13C(5)15N(1) of V [6.013809]</option> + <option value="768">768: Label:13C(6) of I [6.020129]</option> + <option value="769">769: Label:13C(6) of K [6.020129]</option> + <option value="770">770: Label:13C(6) of L [6.020129]</option> + <option value="771">771: Label:13C(6) of R [6.020129]</option> + <option value="772">772: Label:13C(6)+Acetyl of K [48.030694]</option> + <option value="773">773: Label:13C(6)+Dimethyl of K [34.051429]</option> + <option value="774">774: Label:13C(6)+GG of K [120.063056]</option> + <option value="775">775: Label:13C(6)15N(1) of I [7.017164]</option> + <option value="776">776: Label:13C(6)15N(1) of L [7.017164]</option> + <option value="777">777: Label:13C(6)15N(2) of K [8.014199]</option> + <option value="778">778: Label:13C(6)15N(2)+Acetyl of K [50.024764]</option> + <option value="779">779: Label:13C(6)15N(2)+Dimethyl of K [36.045499]</option> + <option value="780">780: Label:13C(6)15N(2)+GG of K [122.057126]</option> + <option value="781">781: Label:13C(6)15N(4) of R [10.008269]</option> + <option value="782">782: Label:13C(6)15N(4)+Dimethyl of R [38.039569]</option> + <option value="783">783: Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) of R [46.083939]</option> + <option value="784">784: Label:13C(6)15N(4)+Methyl of R [24.023919]</option> + <option value="785">785: Label:13C(6)15N(4)+Methyl:2H(3)13C(1) of R [28.046104]</option> + <option value="786">786: Label:13C(9) of F [9.030193]</option> + <option value="787">787: Label:13C(9) of Y [9.030193]</option> + <option value="788">788: Label:13C(9)+Phospho of Y [88.996524]</option> + <option value="789">789: Label:13C(9)15N(1) of F [10.027228]</option> + <option value="790">790: Label:15N(1) of A [0.997035]</option> + <option value="791">791: Label:15N(1) of C [0.997035]</option> + <option value="792">792: Label:15N(1) of D [0.997035]</option> + <option value="793">793: Label:15N(1) of E [0.997035]</option> + <option value="794">794: Label:15N(1) of F [0.997035]</option> + <option value="795">795: Label:15N(1) of G [0.997035]</option> + <option value="796">796: Label:15N(1) of I [0.997035]</option> + <option value="797">797: Label:15N(1) of L [0.997035]</option> + <option value="798">798: Label:15N(1) of M [0.997035]</option> + <option value="799">799: Label:15N(1) of P [0.997035]</option> + <option value="800">800: Label:15N(1) of S [0.997035]</option> + <option value="801">801: Label:15N(1) of T [0.997035]</option> + <option value="802">802: Label:15N(1) of V [0.997035]</option> + <option value="803">803: Label:15N(1) of Y [0.997035]</option> + <option value="804">804: Label:15N(2) of K [1.99407]</option> + <option value="805">805: Label:15N(2) of N [1.99407]</option> + <option value="806">806: Label:15N(2) of Q [1.99407]</option> + <option value="807">807: Label:15N(2) of W [1.99407]</option> + <option value="808">808: Label:15N(2)2H(9) of K [11.050561]</option> + <option value="809">809: Label:15N(3) of H [2.991105]</option> + <option value="810">810: Label:15N(4) of R [3.98814]</option> + <option value="811">811: Label:18O(1) of C-term [2.004246]</option> + <option value="812">812: Label:18O(1) of S [2.004246]</option> + <option value="813">813: Label:18O(1) of T [2.004246]</option> + <option value="814">814: Label:18O(1) of Y [2.004246]</option> + <option value="815">815: Label:18O(2) of C-term [4.008491]</option> + <option value="816">816: Label:2H(10) of L [10.062767]</option> + <option value="817">817: Label:2H(3) of L [3.01883]</option> + <option value="818">818: Label:2H(3) of M [3.01883]</option> + <option value="819">819: Label:2H(3)+Oxidation of M [19.013745]</option> + <option value="820">820: Label:2H(4) of F [4.025107]</option> + <option value="821">821: Label:2H(4) of K [4.025107]</option> + <option value="822">822: Label:2H(4) of Y [4.025107]</option> + <option value="823">823: Label:2H(4)+Acetyl of K [46.035672]</option> + <option value="824">824: Label:2H(4)+GG of K [118.068034]</option> + <option value="825">825: Label:2H(4)13C(1) of R [5.028462]</option> + <option value="826">826: Label:2H(6)15N(1) of P [7.034695]</option> + <option value="827">827: Label:2H(7)15N(4) of R [11.032077]</option> + <option value="828">828: Label:2H(9)13C(6)15N(2) of K [17.07069]</option> + <option value="829">829: lapachenole of C [240.11503]</option> + <option value="830">830: Leu->MetOx of L [33.951335]</option> + <option value="831">831: Lys of N-term [128.094963]</option> + <option value="832">832: Lys->Allysine of K [-1.031634]</option> + <option value="833">833: Lys->AminoadipicAcid of K [14.96328]</option> + <option value="834">834: Lys->CamCys of K [31.935685]</option> + <option value="835">835: Lys->MetOx of K [18.940436]</option> + <option value="836">836: Lys-loss of protein K [-128.094963]</option> + <option value="837">837: Lysbiotinhydrazide of K [241.088497]</option> + <option value="838">838: maleimide of C [97.016378]</option> + <option value="839">839: maleimide of K [97.016378]</option> + <option value="840">840: Malonyl of C [86.000394]</option> + <option value="841">841: Malonyl of S [86.000394]</option> + <option value="842">842: Menadione of C [170.036779]</option> + <option value="843">843: Menadione of K [170.036779]</option> + <option value="844">844: Menadione-HQ of C [172.05243]</option> + <option value="845">845: Menadione-HQ of K [172.05243]</option> + <option value="846">846: MercaptoEthanol of S [60.003371]</option> + <option value="847">847: MercaptoEthanol of T [60.003371]</option> + <option value="848">848: Met->Aha of M [-4.986324]</option> + <option value="849">849: Met->Hpg of M [-21.987721]</option> + <option value="850">850: Met->Hse of M [-29.992806]</option> + <option value="851">851: Met->Hsl of M [-48.003371]</option> + <option value="852">852: Met-loss of protein M [-131.040485]</option> + <option value="853">853: Met-loss+Acetyl of protein M [-89.02992]</option> + <option value="854">854: Methyl of C [14.01565]</option> + <option value="855">855: Methyl of C-term [14.01565]</option> + <option value="856">856: Methyl of D [14.01565]</option> + <option value="857">857: Methyl of E [14.01565]</option> + <option value="858">858: Methyl of H [14.01565]</option> + <option value="859">859: Methyl of I [14.01565]</option> + <option value="860">860: Methyl of K [14.01565]</option> + <option value="861">861: Methyl of L [14.01565]</option> + <option value="862">862: Methyl of N [14.01565]</option> + <option value="863">863: Methyl of N-term [14.01565]</option> + <option value="864">864: Methyl of protein N-term [14.01565]</option> + <option value="865">865: Methyl of Q [14.01565]</option> + <option value="866">866: Methyl of R [14.01565]</option> + <option value="867">867: Methyl of S [14.01565]</option> + <option value="868">868: Methyl of T [14.01565]</option> + <option value="869">869: Methyl+Acetyl:2H(3) of K [59.045045]</option> + <option value="870">870: Methyl+Deamidated of N [14.999666]</option> + <option value="871">871: Methyl+Deamidated of Q [14.999666]</option> + <option value="872">872: Methyl:2H(2) of K [16.028204]</option> + <option value="873">873: Methyl:2H(2) of N-term [16.028204]</option> + <option value="874">874: Methyl:2H(3) of D [17.03448]</option> + <option value="875">875: Methyl:2H(3) of E [17.03448]</option> + <option value="876">876: Methyl:2H(3) of K [17.03448]</option> + <option value="877">877: Methyl:2H(3) of R [17.03448]</option> + <option value="878">878: Methyl:2H(3)+Acetyl:2H(3) of K [62.063875]</option> + <option value="879">879: Methyl:2H(3)13C(1) of K [18.037835]</option> + <option value="880">880: Methyl:2H(3)13C(1) of N-term [18.037835]</option> + <option value="881">881: Methyl:2H(3)13C(1) of R [18.037835]</option> + <option value="882">882: Methylamine of S [13.031634]</option> + <option value="883">883: Methylamine of T [13.031634]</option> + <option value="884">884: Methylmalonylation of S [100.016044]</option> + <option value="885">885: Methylphosphonate of S [77.987066]</option> + <option value="886">886: Methylphosphonate of T [77.987066]</option> + <option value="887">887: Methylphosphonate of Y [77.987066]</option> + <option value="888">888: Methylpyrroline of K [109.052764]</option> + <option value="889">889: methylsulfonylethyl of C [106.00885]</option> + <option value="890">890: methylsulfonylethyl of H [106.00885]</option> + <option value="891">891: methylsulfonylethyl of K [106.00885]</option> + <option value="892">892: Methylthio of K [45.987721]</option> + <option value="893">893: Methylthio of N-term [45.987721]</option> + <option value="894">894: MG-H1 of R [54.010565]</option> + <option value="895">895: mTRAQ of H [140.094963]</option> + <option value="896">896: mTRAQ of K [140.094963]</option> + <option value="897">897: mTRAQ of N-term [140.094963]</option> + <option value="898">898: mTRAQ of S [140.094963]</option> + <option value="899">899: mTRAQ of T [140.094963]</option> + <option value="900">900: mTRAQ of Y [140.094963]</option> + <option value="901">901: mTRAQ:13C(3)15N(1) of H [144.102063]</option> + <option value="902">902: mTRAQ:13C(3)15N(1) of K [144.102063]</option> + <option value="903">903: mTRAQ:13C(3)15N(1) of N-term [144.102063]</option> + <option value="904">904: mTRAQ:13C(3)15N(1) of S [144.102063]</option> + <option value="905">905: mTRAQ:13C(3)15N(1) of T [144.102063]</option> + <option value="906">906: mTRAQ:13C(3)15N(1) of Y [144.102063]</option> + <option value="907">907: mTRAQ:13C(6)15N(2) of H [148.109162]</option> + <option value="908">908: mTRAQ:13C(6)15N(2) of K [148.109162]</option> + <option value="909">909: mTRAQ:13C(6)15N(2) of N-term [148.109162]</option> + <option value="910">910: mTRAQ:13C(6)15N(2) of S [148.109162]</option> + <option value="911">911: mTRAQ:13C(6)15N(2) of T [148.109162]</option> + <option value="912">912: mTRAQ:13C(6)15N(2) of Y [148.109162]</option> + <option value="913">913: MTSL of C [184.07961]</option> + <option value="914">914: Myristoleyl of protein G [208.182715]</option> + <option value="915">915: Myristoyl of C [210.198366]</option> + <option value="916">916: Myristoyl of G [210.198366]</option> + <option value="917">917: Myristoyl of K [210.198366]</option> + <option value="918">918: Myristoyl+Delta:H(-4) of protein G [206.167065]</option> + <option value="919">919: N-dimethylphosphate of S [107.013615]</option> + <option value="920">920: NBS of W [152.988449]</option> + <option value="921">921: NBS:13C(6) of W [159.008578]</option> + <option value="922">922: NDA of K [175.042199]</option> + <option value="923">923: NDA of N-term [175.042199]</option> + <option value="924">924: NEIAA of C [85.052764]</option> + <option value="925">925: NEIAA of Y [85.052764]</option> + <option value="926">926: NEIAA:2H(5) of C [90.084148]</option> + <option value="927">927: NEIAA:2H(5) of Y [90.084148]</option> + <option value="928">928: NEM:2H(5) of C [130.079062]</option> + <option value="929">929: NEM:2H(5)+H2O of C [148.089627]</option> + <option value="930">930: NEMsulfur of C [157.019749]</option> + <option value="931">931: NEMsulfurWater of C [175.030314]</option> + <option value="932">932: Nethylmaleimide+water of C [143.058243]</option> + <option value="933">933: Nethylmaleimide+water of K [143.058243]</option> + <option value="934">934: NIC of K [105.021464]</option> + <option value="935">935: NIC of N-term [105.021464]</option> + <option value="936">936: Nitro of W [44.985078]</option> + <option value="937">937: Nitro of Y [44.985078]</option> + <option value="938">938: Nitrosyl of C [28.990164]</option> + <option value="939">939: Nmethylmaleimide of C [111.032028]</option> + <option value="940">940: Nmethylmaleimide of K [111.032028]</option> + <option value="941">941: Nmethylmaleimide+water of C [129.042593]</option> + <option value="942">942: NP40 of N-term [220.182715]</option> + <option value="943">943: O-Dimethylphosphate of S [107.997631]</option> + <option value="944">944: O-Dimethylphosphate of T [107.997631]</option> + <option value="945">945: O-Dimethylphosphate of Y [107.997631]</option> + <option value="946">946: O-Et-N-diMePhospho of S [135.044916]</option> + <option value="947">947: O-Isopropylmethylphosphonate of S [120.034017]</option> + <option value="948">948: O-Isopropylmethylphosphonate of T [120.034017]</option> + <option value="949">949: O-Isopropylmethylphosphonate of Y [120.034017]</option> + <option value="950">950: O-Methylphosphate of S [93.981981]</option> + <option value="951">951: O-Methylphosphate of T [93.981981]</option> + <option value="952">952: O-Methylphosphate of Y [93.981981]</option> + <option value="953">953: O-pinacolylmethylphosphonate of H [162.080967]</option> + <option value="954">954: O-pinacolylmethylphosphonate of K [162.080967]</option> + <option value="955">955: O-pinacolylmethylphosphonate of S [162.080967]</option> + <option value="956">956: O-pinacolylmethylphosphonate of T [162.080967]</option> + <option value="957">957: O-pinacolylmethylphosphonate of Y [162.080967]</option> + <option value="958">958: Octanoyl of C [126.104465]</option> + <option value="959">959: Octanoyl of S [126.104465]</option> + <option value="960">960: Octanoyl of T [126.104465]</option> + <option value="961">961: Oxidation of D [15.994915]</option> + <option value="962">962: Oxidation of F [15.994915]</option> + <option value="963">963: Oxidation of G [15.994915]</option> + <option value="964">964: Oxidation of H [15.994915]</option> + <option value="965">965: Oxidation of R [15.994915]</option> + <option value="966">966: Oxidation of U [15.994915]</option> + <option value="967">967: Oxidation of W [15.994915]</option> + <option value="968">968: Oxidation of Y [15.994915]</option> + <option value="969">969: Oxidation+NEM of C [141.042593]</option> + <option value="970">970: Palmitoleyl of C [236.214016]</option> + <option value="971">971: Palmitoleyl of S [236.214016]</option> + <option value="972">972: Palmitoleyl of T [236.214016]</option> + <option value="973">973: Palmitoyl of C [238.229666]</option> + <option value="974">974: Palmitoyl of K [238.229666]</option> + <option value="975">975: Palmitoyl of protein N-term [238.229666]</option> + <option value="976">976: Palmitoyl of S [238.229666]</option> + <option value="977">977: Palmitoyl of T [238.229666]</option> + <option value="978">978: PEITC of C [163.04557]</option> + <option value="979">979: PEITC of K [163.04557]</option> + <option value="980">980: PEITC of N-term [163.04557]</option> + <option value="981">981: Pentose of S [132.042259]</option> + <option value="982">982: Pentose of T [132.042259]</option> + <option value="983">983: Pentylamine of Q [85.089149]</option> + <option value="984">984: PET of S [121.035005]</option> + <option value="985">985: PET of T [121.035005]</option> + <option value="986">986: Phe->CamCys of F [12.962234]</option> + <option value="987">987: Phenylisocyanate of N-term [119.037114]</option> + <option value="988">988: Phenylisocyanate:2H(5) of N-term [124.068498]</option> + <option value="989">989: phenylsulfonylethyl of C [168.0245]</option> + <option value="990">990: Phospho of C [79.966331]</option> + <option value="991">991: Phospho of D [79.966331]</option> + <option value="992">992: Phospho of H [79.966331]</option> + <option value="993">993: Phospho of K [79.966331]</option> + <option value="994">994: Phospho of R [79.966331]</option> + <option value="995">995: Phospho of S [79.966331]</option> + <option value="996">996: Phospho of T [79.966331]</option> + <option value="997">997: Phospho of Y [79.966331]</option> + <option value="998">998: PhosphoHex of S [242.019154]</option> + <option value="999">999: PhosphoHex of T [242.019154]</option> + <option value="1000">1000: Phosphopropargyl of S [116.997965]</option> + <option value="1001">1001: Phosphopropargyl of T [116.997965]</option> + <option value="1002">1002: Phosphopropargyl of Y [116.997965]</option> + <option value="1003">1003: phosphoRibosyl of D [212.00859]</option> + <option value="1004">1004: phosphoRibosyl of E [212.00859]</option> + <option value="1005">1005: phosphoRibosyl of R [212.00859]</option> + <option value="1006">1006: Piperidine of K [68.0626]</option> + <option value="1007">1007: Piperidine of N-term [68.0626]</option> + <option value="1008">1008: Pro->pyro-Glu of P [13.979265]</option> + <option value="1009">1009: Pro->Pyrrolidinone of P [-30.010565]</option> + <option value="1010">1010: Pro->Pyrrolidone of P [-27.994915]</option> + <option value="1011">1011: Propargylamine of C-term [37.031634]</option> + <option value="1012">1012: Propargylamine of D [37.031634]</option> + <option value="1013">1013: Propargylamine of E [37.031634]</option> + <option value="1014">1014: Propionamide of N-term [71.037114]</option> + <option value="1015">1015: Propionamide:2H(3) of C [74.055944]</option> + <option value="1016">1016: Propionyl of K [56.026215]</option> + <option value="1017">1017: Propionyl of N-term [56.026215]</option> + <option value="1018">1018: Propionyl of protein N-term [56.026215]</option> + <option value="1019">1019: Propionyl of S [56.026215]</option> + <option value="1020">1020: Propionyl of T [56.026215]</option> + <option value="1021">1021: Propionyl:13C(3) of K [59.036279]</option> + <option value="1022">1022: Propionyl:13C(3) of N-term [59.036279]</option> + <option value="1023">1023: Propiophenone of C [132.057515]</option> + <option value="1024">1024: Propiophenone of H [132.057515]</option> + <option value="1025">1025: Propiophenone of K [132.057515]</option> + <option value="1026">1026: Propiophenone of R [132.057515]</option> + <option value="1027">1027: Propiophenone of S [132.057515]</option> + <option value="1028">1028: Propiophenone of T [132.057515]</option> + <option value="1029">1029: Propiophenone of W [132.057515]</option> + <option value="1030">1030: Propyl of C-term [42.04695]</option> + <option value="1031">1031: Propyl of D [42.04695]</option> + <option value="1032">1032: Propyl of E [42.04695]</option> + <option value="1033">1033: Propyl of K [42.04695]</option> + <option value="1034">1034: Propyl of N-term [42.04695]</option> + <option value="1035">1035: Propyl of protein C-term [42.04695]</option> + <option value="1036">1036: Propyl:2H(6) of K [48.084611]</option> + <option value="1037">1037: Propyl:2H(6) of N-term [48.084611]</option> + <option value="1038">1038: PropylNAGthiazoline of C [232.064354]</option> + <option value="1039">1039: PS_Hapten of C [120.021129]</option> + <option value="1040">1040: PS_Hapten of H [120.021129]</option> + <option value="1041">1041: PS_Hapten of K [120.021129]</option> + <option value="1042">1042: pupylation of K [243.085521]</option> + <option value="1043">1043: PyMIC of N-term [134.048013]</option> + <option value="1044">1044: PyridoxalPhosphate of K [229.014009]</option> + <option value="1045">1045: PyridoxalPhosphateH2 of K [231.02966]</option> + <option value="1046">1046: Pyridylacetyl of K [119.037114]</option> + <option value="1047">1047: Pyridylacetyl of N-term [119.037114]</option> + <option value="1048">1048: Pyro-carbamidomethyl of C [39.994915]</option> + <option value="1049">1049: pyrophospho of S [159.932662]</option> + <option value="1050">1050: pyrophospho of T [159.932662]</option> + <option value="1051">1051: PyruvicAcidIminyl of K [70.005479]</option> + <option value="1052">1052: PyruvicAcidIminyl of protein C [70.005479]</option> + <option value="1053">1053: PyruvicAcidIminyl of protein V [70.005479]</option> + <option value="1054">1054: QAT of C [171.149738]</option> + <option value="1055">1055: QAT:2H(3) of C [174.168569]</option> + <option value="1056">1056: Saligenin of H [106.041865]</option> + <option value="1057">1057: Saligenin of K [106.041865]</option> + <option value="1058">1058: Ser->LacticAcid of protein S [-15.010899]</option> + <option value="1059">1059: SMA of K [127.063329]</option> + <option value="1060">1060: SMA of N-term [127.063329]</option> + <option value="1061">1061: spermidine of Q [128.131349]</option> + <option value="1062">1062: spermine of Q [185.189198]</option> + <option value="1063">1063: SPITC of K [214.971084]</option> + <option value="1064">1064: SPITC of N-term [214.971084]</option> + <option value="1065">1065: SPITC:13C(6) of K [220.991213]</option> + <option value="1066">1066: SPITC:13C(6) of N-term [220.991213]</option> + <option value="1067">1067: Succinyl of K [100.016044]</option> + <option value="1068">1068: Succinyl of N-term [100.016044]</option> + <option value="1069">1069: Succinyl of protein N-term [100.016044]</option> + <option value="1070">1070: Succinyl:13C(4) of K [104.029463]</option> + <option value="1071">1071: Succinyl:13C(4) of N-term [104.029463]</option> + <option value="1072">1072: Succinyl:2H(4) of K [104.041151]</option> + <option value="1073">1073: Succinyl:2H(4) of N-term [104.041151]</option> + <option value="1074">1074: SulfanilicAcid of C-term [155.004099]</option> + <option value="1075">1075: SulfanilicAcid of D [155.004099]</option> + <option value="1076">1076: SulfanilicAcid of E [155.004099]</option> + <option value="1077">1077: SulfanilicAcid:13C(6) of C-term [161.024228]</option> + <option value="1078">1078: SulfanilicAcid:13C(6) of D [161.024228]</option> + <option value="1079">1079: SulfanilicAcid:13C(6) of E [161.024228]</option> + <option value="1080">1080: Sulfide of C [31.972071]</option> + <option value="1081">1081: Sulfide of D [31.972071]</option> + <option value="1082">1082: Sulfide of W [31.972071]</option> + <option value="1083">1083: Sulfo of C [79.956815]</option> + <option value="1084">1084: Sulfo of S [79.956815]</option> + <option value="1085">1085: Sulfo of T [79.956815]</option> + <option value="1086">1086: Sulfo of Y [79.956815]</option> + <option value="1087">1087: sulfo+amino of Y [94.967714]</option> + <option value="1088">1088: SulfurDioxide of C [63.9619]</option> + <option value="1089">1089: Thiadiazole of C [174.025169]</option> + <option value="1090">1090: Thiazolidine of C [12.0]</option> + <option value="1091">1091: Thioacyl of K [87.998285]</option> + <option value="1092">1092: thioacylPA of K [159.035399]</option> + <option value="1093">1093: Thiophospho of S [95.943487]</option> + <option value="1094">1094: Thiophospho of T [95.943487]</option> + <option value="1095">1095: Thiophospho of Y [95.943487]</option> + <option value="1096">1096: Thrbiotinhydrazide of T [240.104482]</option> + <option value="1097">1097: TMAB of K [128.107539]</option> + <option value="1098">1098: TMAB of N-term [128.107539]</option> + <option value="1099">1099: TMAB:2H(9) of K [137.16403]</option> + <option value="1100">1100: TMAB:2H(9) of N-term [137.16403]</option> + <option value="1101">1101: TMT of H [224.152478]</option> + <option value="1102">1102: TMT of K [224.152478]</option> + <option value="1103">1103: TMT of N-term [224.152478]</option> + <option value="1104">1104: TMT of protein N-term [224.152478]</option> + <option value="1105">1105: TMT of S [224.152478]</option> + <option value="1106">1106: TMT of T [224.152478]</option> + <option value="1107">1107: TMT2plex of H [225.155833]</option> + <option value="1108">1108: TMT2plex of K [225.155833]</option> + <option value="1109">1109: TMT2plex of N-term [225.155833]</option> + <option value="1110">1110: TMT2plex of protein N-term [225.155833]</option> + <option value="1111">1111: TMT2plex of S [225.155833]</option> + <option value="1112">1112: TMT2plex of T [225.155833]</option> + <option value="1113">1113: TMT6plex of H [229.162932]</option> + <option value="1114">1114: TMT6plex of K [229.162932]</option> + <option value="1115">1115: TMT6plex of N-term [229.162932]</option> + <option value="1116">1116: TMT6plex of protein N-term [229.162932]</option> + <option value="1117">1117: TMT6plex of S [229.162932]</option> + <option value="1118">1118: TMT6plex of T [229.162932]</option> + <option value="1119">1119: TNBS of K [210.986535]</option> + <option value="1120">1120: TNBS of N-term [210.986535]</option> + <option value="1121">1121: trifluoro of L [53.971735]</option> + <option value="1122">1122: Trimethyl of K [42.04695]</option> + <option value="1123">1123: Trimethyl of protein A [42.04695]</option> + <option value="1124">1124: Trimethyl of R [42.04695]</option> + <option value="1125">1125: Trimethyl:13C(3)2H(9) of K [54.113505]</option> + <option value="1126">1126: Trimethyl:13C(3)2H(9) of R [54.113505]</option> + <option value="1127">1127: Trimethyl:2H(9) of K [51.103441]</option> + <option value="1128">1128: Trimethyl:2H(9) of R [51.103441]</option> + <option value="1129">1129: Trioxidation of W [47.984744]</option> + <option value="1130">1130: Trioxidation of Y [47.984744]</option> + <option value="1131">1131: Tris of N [104.071154]</option> + <option value="1132">1132: Triton of C-term [188.156501]</option> + <option value="1133">1133: Triton of N-term [188.156501]</option> + <option value="1134">1134: Trp->Hydroxykynurenin of W [19.989829]</option> + <option value="1135">1135: Trp->Kynurenin of W [3.994915]</option> + <option value="1136">1136: Trp->Oxolactone of W [13.979265]</option> + <option value="1137">1137: Tween20 of N-term [165.164326]</option> + <option value="1138">1138: Tyr->Dha of Y [-94.041865]</option> + <option value="1139">1139: Ub-amide of C [196.108602]</option> + <option value="1140">1140: Ub-Br2 of C [100.063663]</option> + <option value="1141">1141: Ub-VME of C [173.092617]</option> + <option value="1142">1142: UgiJoullieProGly of D [154.074228]</option> + <option value="1143">1143: UgiJoullieProGly of E [154.074228]</option> + <option value="1144">1144: Xlink:BMOE of C [220.048407]</option> + <option value="1145">1145: Xlink:DFDNB of K [203.998263]</option> + <option value="1146">1146: Xlink:DFDNB of N [203.998263]</option> + <option value="1147">1147: Xlink:DFDNB of Q [203.998263]</option> + <option value="1148">1148: Xlink:DFDNB of R [203.998263]</option> + <option value="1149">1149: Xlink:DMP of K [122.084398]</option> + <option value="1150">1150: Xlink:DMP of protein N-term [122.084398]</option> + <option value="1151">1151: Xlink:DMP-de of K [140.094963]</option> + <option value="1152">1152: Xlink:DMP-de of protein N-term [140.094963]</option> + <option value="1153">1153: Xlink:DMP-s of K [154.110613]</option> + <option value="1154">1154: Xlink:DMP-s of protein N-term [154.110613]</option> + <option value="1155">1155: Xlink:DSS of K [156.078644]</option> + <option value="1156">1156: Xlink:DSS of protein N-term [156.078644]</option> + <option value="1157">1157: Xlink:DSS-NH2 of K [155.094629]</option> + <option value="1158">1158: Xlink:DSS-NH2 of protein N-term [155.094629]</option> + <option value="1159">1159: Xlink:DST of K [132.005873]</option> + <option value="1160">1160: Xlink:DST of protein N-term [132.005873]</option> + <option value="1161">1161: Xlink:DTBPc of K [87.01427]</option> + <option value="1162">1162: Xlink:DTBPc of N [87.01427]</option> + <option value="1163">1163: Xlink:DTBPc of protein N-term [87.01427]</option> + <option value="1164">1164: Xlink:DTBPc of Q [87.01427]</option> + <option value="1165">1165: Xlink:DTBPc of R [87.01427]</option> + <option value="1166">1166: Xlink:DTSSP of K [191.991486]</option> + <option value="1167">1167: Xlink:DTSSP of protein N-term [191.991486]</option> + <option value="1168">1168: Xlink:EGS115 of K [115.026943]</option> + <option value="1169">1169: Xlink:EGS115 of protein N-term [115.026943]</option> + <option value="1170">1170: Xlink:EGS244 of K [244.058303]</option> + <option value="1171">1171: Xlink:EGS244 of protein N-term [244.058303]</option> + <option value="1172">1172: Xlink:SMCC of C [237.100108]</option> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pepquery2.xml Wed Sep 28 13:56:01 2022 +0000 @@ -0,0 +1,931 @@ +<tool id="pepquery2" name="PepQuery2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> + <description>Peptide-centric search engine for novel peptide identification and validation.</description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">pepquery</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Failed" /> + <regex match="Exception" + source="stderr" + level="fatal" + description="java Exception" /> + </stdio> + <command><![CDATA[ +@CMD_IMPORTS@ +#if $req_inputs.db_type.db_type_selector == 'history' + #set $db_file = $re.sub('\s','_',$re.sub('[.][^.]*$','',$req_inputs.db_type.db_file.display_name.split('/')[-1])) + ".fa" + ln -s '$req_inputs.db_type.db_file' '$db_file' && +#end if +#if $req_inputs.ms_dataset.ms_dataset_type == 'history' + @INDEX_SPECTRUM_FILES@ + $index_spectrum_files($ms_index.files_path, $req_inputs.ms_dataset.spectrum_files) && +#elif $req_inputs.ms_dataset.ms_dataset_type == 'indexed' + #if $os.path.exists($os.path.join($req_inputs.ms_dataset.index.extra_files_path, 'summary.txt')) + #set $index_dir = 'index_dir' + ln -s '$req_inputs.ms_dataset.index.extra_files_path' index_dir && + #else + #raise ValueError + #end if +#end if +## PepQuery command +pepquery +#if $validation.task_type == "known" + -s 2 $validation.decoy +#else + -s 1 +#end if +#if $req_inputs.ms_dataset.ms_dataset_type in ['history', 'indexed'] + -ms '$index_dir' +#elif $req_inputs.ms_dataset.ms_dataset_type in ['PepQueryDB', 'public'] + -b '$req_inputs.ms_dataset.dataset' +#end if + +#if $req_inputs.db_type.db_type_selector == 'history' + -db '$db_file' +#else + -db '$req_inputs.db_type.db_id' +#end if +#if $req_inputs.input_type.input_type_selector == 'peptide' + -t '$req_inputs.input_type.input_type_selector' + -i '$req_inputs.input_type.multiple.input' +#else + -t '$req_inputs.input_type.input_type_selector' + #if int(str($req_inputs.input_type.input_type_selector)) == 1 + -i '$req_inputs.input_type.multiple.input' + #else + -i '$req_inputs.input_type.input' + #if int(str($req_inputs.input_type.input_type_selector)) == 2 + #if $req_inputs.input_type.frame == 'None' + -f '0' + #else + -f '$req_inputs.input_type.frame' + #end if + #else + -anno '$req_inputs.input_type.anno' + #end if + #end if +#end if + -indexType $req_inputs.indexType + +#if $modifications.fixed_mod + -fixMod '$modifications.fixed_mod' +#end if +#if $modifications.var_mod + -varMod '$modifications.var_mod' +#end if +#if $digestion.enzyme + -e '$digestion.enzyme' +#end if +#if $digestion.max_missed_cleavages + -c '$digestion.max_missed_cleavages' +#end if + +#if $modifications.max_mods + -maxVar '$modifications.max_mods' +#end if + $modifications.unmodified + $modifications.aa +#if $ms_params.tolerance_params.precursor_tolerance + -tol '$ms_params.tolerance_params.precursor_tolerance' +#end if + +#if $ms_params.tolerance_params.precursor_unit + -tolu '$ms_params.tolerance_params.precursor_unit' +#end if +#if $ms_params.tolerance_params.tolerance + -itol '$ms_params.tolerance_params.tolerance' +#end if +#if $ms_params.search.frag_method + -fragmentMethod '$ms_params.search.frag_method' +#end if +#if $ms_params.search.scoring_method + -m '$ms_params.search.scoring_method' +#end if + $ms_params.search.extra_score_validation +#if $ms_params.search.max_charge + -maxCharge '$ms_params.search.max_charge' +#end if +#if $ms_params.search.min_charge + -minCharge '$ms_params.search.min_charge' +#end if +#if $ms_params.search.min_peaks + -minPeaks '$ms_params.search.min_peaks' +#end if +#if $ms_params.search.isotope_error + -ti '$ms_params.search.isotope_error' +#end if +#if $ms_params.search.min_score + -minScore '$ms_params.search.min_score' +#end if +#if $ms_params.search.min_length + -minLength '$ms_params.search.min_length' +#end if +#if $ms_params.search.max_length + -maxLength '$ms_params.search.max_length' +#end if +#if $ms_params.search.num_random_peptides + -n '$ms_params.search.num_random_peptides' +#end if +#if 'psm_annotation.txt' in $outputs_selected + -plot +#end if + $fast + -o pepquery_output + | sed 's/No valid peptide/Error: No valid peptide/' | tee >(cat 1>&2) + ]]> + </command> + <inputs> + <conditional name="validation"> + <param name="task_type" argument="-s" type="select" label="Validation Task Type"> + <option value="novel" selected="true">novel peptide/protein validation</option> + <option value="known">known peptide/protein validation</option> + </param> + <when value="novel"/> + <when value="known"> + <param name="decoy" argument="-decoy" type="boolean" truevalue="-decoy" falsevalue="" checked="false" label="Identity the decoy version of the selected target protein"/> + </when> + </conditional> + <section name="req_inputs" title="Input Data" expanded="true"> + <conditional name="input_type"> + <param name="input_type_selector" argument="-t" type="select" label="Input Type" help="" > + <option value="peptide">peptide</option> + <option value="1">protein</option> + <option value="2">DNA (translate to protein sequences)</option> + <!-- these are not working with pepquery version 1.6 + <option value="3">VCF (translate to protein sequences)</option> + <option value="4">BED (translate to protein sequences)</option> + <option value="5">GTF (translate to protein sequences)</option> + --> + </param> + <when value="peptide"> + <conditional name="multiple"> + <param name="peptide_input_selector" type="select" label="Peptides?"> + <option value="multiple">Peptide list from your history</option> + <option value="single">Single peptide entered as text</option> + </param> + <when value="multiple"> + <param name="input" argument="-i" type="data" format="txt" label="Peptide Sequences (.txt)" help="Peptide sequence file containing peptides which you want to search (no column header, 1 peptide per line)." /> + </when> + <when value="single"> + <param name="input" argument="-i" type="text" label="Peptide Sequence" help="Peptide sequence(s) which you want to search"> + <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+(,[AC-IK-NP-TV-Yac-ik-np-tv-y]+)*$</validator> + </param> + </when> + </conditional> + </when> + <when value="1"> + <conditional name="multiple"> + <param name="protein_input_selector" type="select" label="Proteins?"> + <option value="multiple">Protein fasta from your history</option> + <option value="single">Single protein entered as text</option> + </param> + <when value="multiple"> + <param name="input" argument="-i" type="data" format="fasta" label="Protein Sequences (.txt)" help="Protein fasta file containing proteins which you want to search." /> + </when> + <when value="single"> + <param name="input" argument="-i" type="text" label="Protein Sequence" help="Protein sequence which you want to search"> + <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+$</validator> + </param> + </when> + </conditional> + </when> + <when value="2"> + <param name="input" argument="-i" type="text" label="DNA Sequence (at least 60 bp)" help="DNA sequence which you want to search"> + <validator type="regex" message="Must be at least 60bp">^[acgtuAGCTU]{60}[acgtuAGCTU]*$</validator> + </param> + <param name="frame" argument="-f" type="select" label="Frame(s) for DNA translation" multiple="true" help="The frame(s) to translate DNA sequence to protein. Selecting nothing (default) keeps the longest frame"> + <option value="1">1</option> + <option value="2">2</option> + <option value="3">3</option> + <option value="4">4</option> + <option value="5">5</option> + <option value="6">6</option> + </param> + </when> + <!-- these are not working with pepquery version 1.6 + <when value="3"> + <param name="input" type="data" format="vcf" label="VCF File" argument="-i" help="" /> + <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the VCF file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" /> + </when> + <when value="4"> + <param name="input" type="data" format="bed" label="BED File" argument="-i" help="" /> + <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the BED file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" /> + </when> + <when value="5"> + <param name="input" type="data" format="gtf" label="GTF File" argument="-i" help="" /> + <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the GTF file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" /> + </when> + --> + </conditional> + <conditional name="db_type"> + <param name="db_type_selector" type="select" label="Protein Reference Database from" help="" > + <option value="history">history</option> + <option value="download">download</option> + </param> + <when value="history"> + <param name="db_file" argument="-db" type="data" format="fasta" label="Protein Reference Database File" help="an input sequence that matches a reference will be ignored." /> + </when> + <when value="download"> + <param name="db_id" type="text" value="" label="Public protein sequence database"> + <help>Currently supported dowloads: gencode:human, swissprot:human, refseq:human</help> + <option value="gencode:human">gencode:human</option> + <option value="swissprot:human">swissprot:human</option> + <option value="refseq:human">refseq:human</option> + <validator type="regex" message="">^(swissprot|refseq|gencode):(human)$</validator> + </param> + </when> + </conditional> + <conditional name="ms_dataset"> + <param name="ms_dataset_type" type="select" label="MS/MS dataset to search" help="" > + <option value="history"> Spectrum Datasets from history</option> + <option value="indexed">Indexed MS/MS spectrums</option> + <option value="PepQueryDB">PepQueryDB</option> + <option value="public">public proteomics data repositories</option> + </param> + <when value="history"> + <param name="spectrum_files" argument="-ms" type="data" format="mgf,mzml,mzxml,thermo.raw" label="Spectrum File" help="Spectrum file used for identification, formats: MGF,mzML,mzXML,Thermo RAW" /> + </when> + <when value="indexed"> + <param name="index" argument="-ms" type="data" format="txt" label="PepQuery Index" help="" /> + </when> + <when value="PepQueryDB"> + <param name="dataset" argument="-b" type="text" value="" label="PepQueryDB dataset"> + <option value="all">all</option> + <option value="w">w:global proteome</option> + <option value="p">p:phosphorylation</option> + <option value="a">a:acetylation</option> + <option value="u">u:ubiquitination</option> + <option value="g">g:glycosylation</option> + <option value="Academia_Sinica_LUAD100_Phosphoproteome_PDC000220">Academia_Sinica_LUAD100_Phosphoproteome_PDC000220</option> + <option value="Academia_Sinica_LUAD100_Proteome_PDC000219">Academia_Sinica_LUAD100_Proteome_PDC000219</option> + <option value="CCLE_proteome_MSV000085836">CCLE_proteome_MSV000085836</option> + <option value="CPTAC">CPTAC</option> + <option value="CPTAC_CCRCC_Discovery_Study_Phosphoproteme_PDC000128">CPTAC_CCRCC_Discovery_Study_Phosphoproteme_PDC000128</option> + <option value="CPTAC_CCRCC_Discovery_Study_Proteome_PDC000127">CPTAC_CCRCC_Discovery_Study_Proteome_PDC000127</option> + <option value="CPTAC_GBM_Discovery_Study_Acetylome_PDC000245">CPTAC_GBM_Discovery_Study_Acetylome_PDC000245</option> + <option value="CPTAC_GBM_Discovery_Study_Phosphoproteome_PDC000205">CPTAC_GBM_Discovery_Study_Phosphoproteome_PDC000205</option> + <option value="CPTAC_GBM_Discovery_Study_Proteome_PDC000204">CPTAC_GBM_Discovery_Study_Proteome_PDC000204</option> + <option value="CPTAC_HNSCC_Discovery_Study_Phosphoproteome_PDC000222">CPTAC_HNSCC_Discovery_Study_Phosphoproteome_PDC000222</option> + <option value="CPTAC_HNSCC_Discovery_Study_Proteome_PDC000221">CPTAC_HNSCC_Discovery_Study_Proteome_PDC000221</option> + <option value="CPTAC_LSCC_Discovery_Study_Acetylome_PDC000233">CPTAC_LSCC_Discovery_Study_Acetylome_PDC000233</option> + <option value="CPTAC_LSCC_Discovery_Study_Phosphoproteome_PDC000232">CPTAC_LSCC_Discovery_Study_Phosphoproteome_PDC000232</option> + <option value="CPTAC_LSCC_Discovery_Study_Proteome_PDC000234">CPTAC_LSCC_Discovery_Study_Proteome_PDC000234</option> + <option value="CPTAC_LSCC_Discovery_Study_Ubiquitylome_PDC000237">CPTAC_LSCC_Discovery_Study_Ubiquitylome_PDC000237</option> + <option value="CPTAC_LUAD_Discovery_Study_Acetylome_PDC000224">CPTAC_LUAD_Discovery_Study_Acetylome_PDC000224</option> + <option value="CPTAC_LUAD_Discovery_Study_Phosphoproteome_PDC000149">CPTAC_LUAD_Discovery_Study_Phosphoproteome_PDC000149</option> + <option value="CPTAC_LUAD_Discovery_Study_Proteome_PDC000153">CPTAC_LUAD_Discovery_Study_Proteome_PDC000153</option> + <option value="CPTAC_PDA_Discovery_Study_Phosphoproteome_PDC000271">CPTAC_PDA_Discovery_Study_Phosphoproteome_PDC000271</option> + <option value="CPTAC_PDA_Discovery_Study_Proteome_PDC000270">CPTAC_PDA_Discovery_Study_Proteome_PDC000270</option> + <option value="CPTAC_Pediatric_Brain_Cancer_Pilot_Study_Phosphoproteome_PDC000176">CPTAC_Pediatric_Brain_Cancer_Pilot_Study_Phosphoproteome_PDC000176</option> + <option value="CPTAC_Pediatric_Brain_Cancer_Pilot_Study_Proteome_PDC000180">CPTAC_Pediatric_Brain_Cancer_Pilot_Study_Proteome_PDC000180</option> + <option value="CPTAC_Prospective_Breast_BI_Acetylome_PDC000239">CPTAC_Prospective_Breast_BI_Acetylome_PDC000239</option> + <option value="CPTAC_Prospective_Breast_BI_Phosphoproteome_PDC000121">CPTAC_Prospective_Breast_BI_Phosphoproteome_PDC000121</option> + <option value="CPTAC_Prospective_Breast_BI_Proteome_PDC000120">CPTAC_Prospective_Breast_BI_Proteome_PDC000120</option> + <option value="CPTAC_Prospective_Colon_PNNL_Phosphoproteome_PDC000117">CPTAC_Prospective_Colon_PNNL_Phosphoproteome_PDC000117</option> + <option value="CPTAC_Prospective_Colon_PNNL_Proteome_PDC000116">CPTAC_Prospective_Colon_PNNL_Proteome_PDC000116</option> + <option value="CPTAC_Prospective_Colon_VU_Proteome_PDC000109">CPTAC_Prospective_Colon_VU_Proteome_PDC000109</option> + <option value="CPTAC_Prospective_Ovarian_JHU_Glycoproteome_PDC000251">CPTAC_Prospective_Ovarian_JHU_Glycoproteome_PDC000251</option> + <option value="CPTAC_Prospective_Ovarian_JHU_Proteome_PDC000110">CPTAC_Prospective_Ovarian_JHU_Proteome_PDC000110</option> + <option value="CPTAC_Prospective_Ovarian_PNNL_Phosphoproteome_PDC000119">CPTAC_Prospective_Ovarian_PNNL_Phosphoproteome_PDC000119</option> + <option value="CPTAC_Prospective_Ovarian_PNNL_Proteome_Qeplus_PDC000118">CPTAC_Prospective_Ovarian_PNNL_Proteome_Qeplus_PDC000118</option> + <option value="CPTAC_TCGA_Breast_Cancer_Phosphoproteome_PDC000174">CPTAC_TCGA_Breast_Cancer_Phosphoproteome_PDC000174</option> + <option value="CPTAC_TCGA_Breast_Cancer_Proteome_PDC000173">CPTAC_TCGA_Breast_Cancer_Proteome_PDC000173</option> + <option value="CPTAC_TCGA_Colon_Cancer_Proteome_PDC000111">CPTAC_TCGA_Colon_Cancer_Proteome_PDC000111</option> + <option value="CPTAC_TCGA_Ovarian_Glycoproteome_PDC000112">CPTAC_TCGA_Ovarian_Glycoproteome_PDC000112</option> + <option value="CPTAC_TCGA_Ovarian_Phosphoproteome_PDC000115">CPTAC_TCGA_Ovarian_Phosphoproteome_PDC000115</option> + <option value="CPTAC_TCGA_Ovarian_Proteome_PDC000113_PDC000114">CPTAC_TCGA_Ovarian_Proteome_PDC000113_PDC000114</option> + <option value="CPTAC_UCEC_Discovery_Study_Acetylome_PDC000226">CPTAC_UCEC_Discovery_Study_Acetylome_PDC000226</option> + <option value="CPTAC_UCEC_Discovery_Study_Phosphoproteome_PDC000126">CPTAC_UCEC_Discovery_Study_Phosphoproteome_PDC000126</option> + <option value="CPTAC_UCEC_Discovery_Study_Proteome_PDC000125">CPTAC_UCEC_Discovery_Study_Proteome_PDC000125</option> + <option value="Deep_29_healthy_human_tissues_PXD010154">Deep_29_healthy_human_tissues_PXD010154</option> + <option value="GTEx_32_Tissues_Proteome_PXD016999">GTEx_32_Tissues_Proteome_PXD016999</option> + <option value="HBV_Related_Hepatocellular_Carcinoma_Phosphoproteome_PDC000199">HBV_Related_Hepatocellular_Carcinoma_Phosphoproteome_PDC000199</option> + <option value="HBV_Related_Hepatocellular_Carcinoma_Proteome_PDC000198">HBV_Related_Hepatocellular_Carcinoma_Proteome_PDC000198</option> + <option value="Oral_Squamous_Cell_Carcinoma_Study_Proteome_PDC000262">Oral_Squamous_Cell_Carcinoma_Study_Proteome_PDC000262</option> + <option value="Proteogenomics_of_Gastric_Cancer_Glycoproteome_PDC000216">Proteogenomics_of_Gastric_Cancer_Glycoproteome_PDC000216</option> + <option value="Proteogenomics_of_Gastric_Cancer_Phosphoproteome_PDC000215">Proteogenomics_of_Gastric_Cancer_Phosphoproteome_PDC000215</option> + <option value="Proteogenomics_of_Gastric_Cancer_Proteome_PDC000214">Proteogenomics_of_Gastric_Cancer_Proteome_PDC000214</option> + </param> + </when> + <when value="public"> + <param name="dataset" type="text" value="" label="Public dataset"> + <validator type="regex" message="An identifier strating with PXD or MSV or JPST">^(PXD|MSV|JPST).*$</validator> + </param> + </when> + </conditional> + + <param name="indexType" argument="-indexType" type="select" label="Report Spectrum Scan as" help="" > + <option value="1" selected="true">index (1-based) in MGF</option> + <option value="2">spectrum title in MGF</option> + </param> + </section> + + <param name="parameter_set" argument="-p" type="text" value="" optional="true" label="MS/MS searching parameter set name"> + <help>Currently supported set names start with: MS1 or TMT</help> + <option value="MS1_H_MS2_H_LF">MS1_H_MS2_H_LF</option> + <option value="MS1_H_MS2_L_LF">MS1_H_MS2_L_LF</option> + <option value="TMT10_11">TMT10_11</option> + <option value="TMT10_11_MS2_L">TMT10_11_MS2_L</option> + <option value="TMT10_11_MS2_L_phosphorylation">TMT10_11_MS2_L_phosphorylation</option> + <option value="TMT10_11_acetylation">TMT10_11_acetylation</option> + <option value="TMT10_11_glycosylation">TMT10_11_glycosylation</option> + <option value="TMT10_11_phosphorylation">TMT10_11_phosphorylation</option> + <option value="TMT10_11_ubiquitination">TMT10_11_ubiquitination</option> + </param> + +<!-- +TMT10_11_MS2_L_phosphorylation + Fixed modification: 1,11,12 = Carbamidomethylation of C,TMT 10-plex of K,TMT 10-plex of peptide N-term + Variable modification: 2,7,8,9 = Oxidation of M,Phosphorylation of S,Phosphorylation of T,Phosphorylation of Y + Enzyme: 1 + Max Missed cleavages: 1 + Precursor mass tolerance: 20.0 + Precursor ion mass tolerance unit: ppm + Fragment ion mass tolerance: 0.6 + Fragment ion mass tolerance unit: Da +--> + + <section name="modifications" title="Modifications" expanded="false"> + <param name="fixed_mod" argument="-fixMod" type="select" label="Fixed modification(s)" multiple="true" optional="true"> + <help>default: 1: Carbamidomethylation of C [57.02146372057]</help> + <expand macro="modifications" /> + </param> + <param name="var_mod" argument="-varMod" type="select" label="Variable modification(s)" multiple="true" optional="true"> + <help>default: 2: Oxidation of M [15.99491461956]</help> + <expand macro="modifications" /> + </param> + + <param name="max_mods" argument="-maxVar" type="integer" label="Max Modifications" value="" min="0" max="10" optional="true" help="Max number of variable modifications Default: 3" /> + <param name="unmodified" argument="-hc" type="boolean" truevalue="-hc" falsevalue="" checked="false" label="Use more stringent criterion for unrestricted modification searching" help="TRUE: score(UMS)>=score(targetPSM); FALSE: score(UMS)>score(targetPSM)" /> + <param name="aa" argument="-aa" type="boolean" truevalue="-aa" falsevalue="" checked="false" label="Consider amino acid substitution modifications?" help="Whether or not to consider aa substitution modifications when perform modification filtering." /> + </section> + + <section name="digestion" title="Digestion" expanded="false"> + <param name="enzyme" argument="-e" type="select" optional="true" label="Enzyme" help="Enzyme used for protein digestion" > + <option value="0">Non enzyme</option> + <option value="1" selected="true">Trypsin</option> + <option value="2">Trypsin (no P rule)</option> + <option value="3">Arg-C</option> + <option value="4">Arg-C (no P rule)</option> + <option value="5">Arg-N</option> + <option value="6">Glu-C</option> + <option value="7">Lys-C</option> + </param> + <param name="max_missed_cleavages" argument="-c" type="integer" value="" optional="true" label="Max Missed Cleavages" help="The max missed cleavages" /> + </section> + + <section name="ms_params" title="Mass spectrometer" expanded="false"> + <section name="tolerance_params" title="Tolerance" expanded="true"> + <param name="precursor_tolerance" argument="-tol" type="integer" value="" optional="true" label="Precursor Tolerance" help="The error window on experimental peptide mass values. This parameter is usually set according to the mass spectrometer which was used to generate the MS/MS data. Default: 10" /> + <param name="precursor_unit" argument="-tolu" type="select" optional="true" label="Precursor Unit" help="The unit of precursor ion m/z tolerance"> + <option value="ppm" selected="true">ppm</option> + <option value="Da">Da</option> + </param> + <param name="tolerance" argument="-itol" type="float" value="0.6" optional="true" label="Tolerance" help="Error window for MS/MS fragment ion mass values in Da unit. Default: 0.6 Da" /> + </section> + + <section name="search" title="PSM" expanded="false"> + <param name="frag_method" argument="-fragmentMethod" type="select" optional="true" label="Fragmentation Method"> + <option value="1" selected="true">CID/HCD</option> + <option value="2">ETD</option> + </param> + <param name="scoring_method" argument="-m" type="select" optional="true" label="Scoring Method"> + <option value="1" selected="true">HyperScore</option> + <option value="2">MVH</option> + </param> + <param name="extra_score_validation" argument="-x" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Add extra score validation" help="use two scoring algorithms for peptide identification" /> + <param name="min_charge" argument="-minCharge" type="integer" value="" optional="true" label="Minimum Charge" help="The minimum charge to consider if the charge state is not available. Default: 2"/> + <param name="max_charge" argument="-maxCharge" type="integer" value="" optional="true" label="Maximum Charge" help="The maximum charge to consider if the charge state is not available. Default: 2" /> + <param name="min_peaks" argument="-minPeaks" type="integer" value="" optional="true" label="Minimum Peaks" help="Min peaks in spectrum. Default: 10" /> + <param name="isotope_error" argument="-ti" type="text" value="" optional="true" label="Isotope peak error range"> + <help>A comma-sepated range of integers from -2 to 2, e.g. '-1,0,1,2' Default: 0</help> + <validator type="regex" message="">^((-2,)?-1,)?0(,1(,2)?)?$</validator> + </param> + <param name="min_score" argument="-minScore" type="integer" value="" min="0" optional="true" label="Minimum Score" help="Minimum score to consider for peptide searching. Default: 12" /> + <param name="min_length" argument="-minLength" type="integer" value="" min="0" optional="true" label="Minimum length of peptide" help="The maximum length of peptide to consider. Default: 7" /> + <param name="max_length" argument="-maxLength" type="integer" value="" min="0" optional="true" label="Maximum length of peptide" help="The maximum length of peptide to consider. Default: 45" /> + <param name="num_random_peptides" argument="-n" type="integer" value="" min="0" optional="true" label="Number of Random Peptides" help="The number of random peptides. Default: 1000" /> + </section> + </section> + + <param name="outputs_selected" type="select" multiple="true" optional="false" label="Select outputs"> + <option value="parameter.txt" selected="true">parameter.txt</option> + <option value="psm.txt" selected="true">psm.txt</option> + <option value="psm_rank.txt" selected="true">psm_rank.txt</option> + <option value="psm_rank.mgf" selected="true">psm_rank.mgf</option> + <option value="psm_annotation.txt" selected="true">psm_annotation.txt</option> + <option value="psm_type.txt" selected="false">psm_type.txt</option> + <option value="detail.txt" selected="true">detail.txt</option> + <option value="ptm.txt" selected="true">ptm.txt</option> + <option value="ptm_detail.txt" selected="true">ptm_detail.txt</option> + <option value="ptm_detail.txt" selected="true">ptm_detail.txt</option> + <option value="ms_index" selected="true">MS/MS Index</option> + </param> + <param name="fast" argument="-fast" type="boolean" truevalue="-fast" falsevalue="" checked="false" label="Use fast mode for searching" help="In fast mode, only one better match from reference peptide-based competitive filtering steps will be returned. A peptide identified or not is not affected by this setting. For most applications, fast mode will speed up the analysis." /> + </inputs> + <outputs> + <data name="ms_index" format="txt" label="${tool.name} on ${on_string}: index summary.txt" from_work_dir="index_dir/summary.txt"> + <filter>'ms_index' in outputs_selected and req_inputs['ms_dataset']['ms_dataset_type'] == 'history'</filter> + </data> + <data name="parameter_txt" format="txt" from_work_dir="pepquery_output/parameter.txt" label="${tool.name} on ${on_string}: parameter.txt"> + <filter>'parameter.txt' in outputs_selected</filter> + </data> + + <data name="psm_txt" format="tabular" from_work_dir="pepquery_output/psm.txt" label="${tool.name} on ${on_string}: psm.txt"> + <filter>'psm.txt' in outputs_selected</filter> + <actions> + <action name="comment_lines" type="metadata" default="1" /> + <action name="column_names" type="metadata" default="peptide,modification,n,spectrum_title,charge,exp_mass,tol_ppm,tol_da,isotope_error,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue" /> + </actions> + </data> + + <data name="psm_rank_txt" format="tabular" from_work_dir="pepquery_output/psm_rank.txt" label="${tool.name} on ${on_string}: psm_rank.txt"> + <filter>'psm_rank.txt' in outputs_selected</filter> + <actions> + <action name="comment_lines" type="metadata" default="1" /> + <action name="column_names" type="metadata" default="peptide,modification,n,spectrum_title,charge,exp_mass,tol_ppm,tol_da,isotope_error,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue,rank,n_ptm,confident,ref_delta_score,mod_delta_score" /> + </actions> + </data> + + <data name="psm_rank_mgf" format="mgf" from_work_dir="pepquery_output/psm_rank.mgf" label="${tool.name} on ${on_string}: psm_rank.mgf"> + <filter>'psm_rank.mgf' in outputs_selected</filter> + </data> + <data name="psm_type_txt" format="tabular" from_work_dir="pepquery_output/psmi_type.txt" label="${tool.name} on ${on_string}: psm_type.txt"> + <filter>'psm_type.txt' in outputs_selected</filter> + <actions> + <action name="comment_lines" type="metadata" default="1" /> + <action name="column_names" type="metadata" default="peptide,spectrum_title,type" /> + </actions> + </data> + <data name="psm_annotation_txt" format="tabular" from_work_dir="pepquery_output/psm_annotation.txt" label="${tool.name} on ${on_string}: psm_annotation.txt"> + <filter>'psm_annotation.txt' in outputs_selected</filter> + <actions> + <action name="comment_lines" type="metadata" default="1" /> + <action name="column_names" type="metadata" default="peptide,modification,Query,calc_mr,observed_mz,charge,pepSeq,m_label,m_mz,m_intensity,mz,intensity" /> + </actions> + </data> + <data name="detail_txt" format="tabular" from_work_dir="pepquery_output/detail.txt" label="${tool.name} on ${on_string}: detail.txt"> + <filter>'detail.txt' in outputs_selected</filter> + <actions> + <action name="comment_lines" type="metadata" default="1" /> + <action name="column_names" type="metadata" default="spectrum_title,peptide,modification,exp_mass,pep_mass,tol_ppm,tol_da,isotope_error,score" /> + </actions> + </data> + + <data name="ptm_txt" format="tabular" from_work_dir="pepquery_output/ptm.txt" label="${tool.name} on ${on_string}: ptm.txt"> + <filter>'ptm.txt' in outputs_selected</filter> + <actions> + <action name="comment_lines" type="metadata" default="1" /> + <action name="column_names" type="metadata" default="spectrum_title,peptide,charge,exp_mass,pep_mass,tol_ppm,tol_da,isotope_error,modification,score" /> + </actions> + </data> + <data name="ptm_detail_txt" format="tabular" from_work_dir="pepquery_output/ptm_detail.txt" label="${tool.name} on ${on_string}: ptm_detail.txt"> + <filter>'ptm_detail.txt' in outputs_selected</filter> + <actions> + <action name="comment_lines" type="metadata" default="1" /> + <action name="column_names" type="metadata" default="peptide,modification,n,spectrum_title,charge,exp_mass,tol_ppm,tol_da,isotope_error,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue,rank,ptm_spectrum_title,ptm_peptide,ptm_charge,ptm_exp_mass,ptm_pep_mass,ptm_tol_ppm,ptm_tol_da,ptm_isotope_error,ptm_modification,ptm_score" /> + </actions> + </data> + + </outputs> + <tests> + <!-- Test-1 --> +<!-- + <test> + <section name="req_inputs"> + <conditional name="input_type"> + <param name="input_type_selector" value="peptide"/> + <conditional name="multiple"> + <param name="peptide_input_selector" value="single" /> + <param name="input" value="ELGSSDLTAR"/> + </conditional> + </conditional> + <param name="db_file" ftype="fasta" value="Uniprot.fasta"/> + <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/> + </section> + <section name="modifications"> + <param name="fixed_mod" value="6,103,157"/> + <param name="var_mod" value="117"/> + <param name="max_mods" value="3"/> + <param name="unmodified" value="False"/> + <param name="aa" value="True"/> + </section> + <section name="ms_params"> + <section name="tolerance_params"> + <param name="precursor_tolerance" value="10"/> + <param name="precursor_unit" value="ppm"/> + <param name="tolerance" value="0.6"/> + </section> + <section name="digestion"> + <param name="enzyme" value="0"/> + <param name="max_missed_cleavages" value="2"/> + </section> + <section name="search"> + <param name="frag_method" value="1"/> + <param name="scoring_method" value="1"/> + <param name="max_charge" value="3"/> + <param name="min_charge" value="2"/> + <param name="min_peaks" value="10"/> + <param name="min_score" value="12"/> + <param name="max_length" value="45"/> + <param name="num_random_peptides" value="1000"/> + </section> + </section> + <output name="psm_rank_txt"> + <assert_contents> + <has_text text="ELGSSDLTAR" /> + <has_line_matching expression="ELGSSDLTAR\tiTRAQ 4-plex of peptide N-term@0\S+\t2\tiTRAQ_f4.mgf\t2\t2\t1191.6\d+\t2.0\d+\t1191.62\d+\t596.81\d+\t18.68\d+\t0\t20\t5\t995\t0.006\d+\t1"/> + </assert_contents> + </output> + </test> +--> + + <!-- Test-2 --> +<!-- + <test> + <section name="req_inputs"> + <conditional name="input_type"> + <param name="input_type_selector" value="peptide"/> + <conditional name="multiple"> + <param name="peptide_input_selector" value="multiple" /> + <param name="input" ftype="tabular" value="novel_peptides"/> + </conditional> + </conditional> + <param name="db_file" ftype="fasta" value="Uniprot.fasta"/> + <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/> + </section> + <section name="modifications"> + <param name="fixed_mod" value="6,103,157"/> + <param name="var_mod" value="117"/> + <param name="max_mods" value="3"/> + <param name="unmodified" value="False"/> + <param name="aa" value="True"/> + </section> + <section name="ms_params"> + <section name="tolerance_params"> + <param name="precursor_tolerance" value="10"/> + <param name="precursor_unit" value="ppm"/> + <param name="tolerance" value="0.6"/> + </section> + <section name="digestion"> + <param name="enzyme" value="0"/> + <param name="max_missed_cleavages" value="2"/> + </section> + <section name="search"> + <param name="frag_method" value="1"/> + <param name="scoring_method" value="1"/> + <param name="max_charge" value="3"/> + <param name="min_charge" value="2"/> + <param name="min_peaks" value="10"/> + <param name="min_score" value="12"/> + <param name="max_length" value="45"/> + <param name="num_random_peptides" value="1000"/> + </section> + </section> + <output name="psm_rank_txt"> + <assert_contents> + <has_text text="ELGSSDLTAR" /> + <has_text text="SPYREFTDHLVK" /> + <has_line_matching expression="SPYREFTDHLVK\tiTRAQ 4-plex of K@12\S+;iTRAQ 4-plex of peptide N-term@0\S+\t1\tiTRAQ_f4.mgf\t4\t3\t1778.\d+\t3.02\d+\t1778.95\d+\t593.99\d+\t12.17\d+\t2\t14\t-1\t-1\t100.0\t1"/> + </assert_contents> + </output> + </test> +--> + + <!-- Test-3 --> +<!-- + <test> + <section name="req_inputs"> + <conditional name="input_type"> + <param name="input_type_selector" value="peptide"/> + <conditional name="multiple"> + <param name="peptide_input_selector" value="multiple" /> + <param name="input" ftype="tabular" value="novel_peptides"/> + </conditional> + </conditional> + <param name="db_file" ftype="fasta" value="Uniprot.fasta"/> + <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/> + </section> + <section name="modifications"> + <param name="fixed_mod" value="6,103,157"/> + <param name="var_mod" value="117"/> + <param name="max_mods" value="3"/> + <param name="unmodified" value="True"/> + <param name="aa" value="True"/> + </section> + <section name="ms_params"> + <section name="tolerance_params"> + <param name="precursor_tolerance" value="10"/> + <param name="precursor_unit" value="ppm"/> + <param name="tolerance" value="0.6"/> + </section> + <section name="digestion"> + <param name="enzyme" value="0"/> + <param name="max_missed_cleavages" value="1"/> + </section> + <section name="search"> + <param name="frag_method" value="1"/> + <param name="scoring_method" value="1"/> + <param name="max_charge" value="3"/> + <param name="min_charge" value="2"/> + <param name="min_peaks" value="7"/> + <param name="min_score" value="10"/> + <param name="max_length" value="45"/> + <param name="num_random_peptides" value="1000"/> + </section> + </section> + <output name="psm_rank_txt"> + <assert_contents> + <has_text text="ELGSSDLTAR" /> + <has_text text="SPYREFTDHLVK" /> + <has_line_matching expression="ELGSSDLTAR\tiTRAQ 4-plex of peptide N-term@0\S+\t2\t3\t2\t1191.6\d+\t-3.04\d+\t1191.62\d+\t596.8\d+\t24.18\d+\t0\t22\t1\t995\t0.002\d+\t1\t0\tYes" /> + </assert_contents> + </output> + </test> +--> + + <!-- Test-4 --> +<!-- + <test> + <section name="req_inputs"> + <conditional name="input_type"> + <param name="input_type_selector" value="1"/> + <conditional name="multiple"> + <param name="protein_input_selector" value="multiple" /> + <param name="input" ftype="fasta" value="novel_proteins.fa"/> + </conditional> + </conditional> + <param name="db_file" ftype="fasta" value="Uniprot.fasta"/> + <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/> + </section> + <section name="modifications"> + <param name="fixed_mod" value="6,103,157"/> + <param name="var_mod" value="117"/> + <param name="max_mods" value="3"/> + <param name="unmodified" value="False"/> + <param name="aa" value="True"/> + </section> + <section name="ms_params"> + <section name="tolerance_params"> + <param name="precursor_tolerance" value="10"/> + <param name="precursor_unit" value="ppm"/> + <param name="tolerance" value="0.6"/> + </section> + <section name="digestion"> + <param name="enzyme" value="0"/> + <param name="max_missed_cleavages" value="2"/> + </section> + <section name="search"> + <param name="frag_method" value="1"/> + <param name="scoring_method" value="1"/> + <param name="max_charge" value="3"/> + <param name="min_charge" value="2"/> + <param name="min_peaks" value="10"/> + <param name="min_score" value="12"/> + <param name="max_length" value="45"/> + <param name="num_random_peptides" value="1000"/> + </section> + </section> + <output name="psm_rank_txt"> + <assert_contents> + <has_text text="ELGSSDLTAR" /> + <has_text text="SPYREFTDHLVK" /> + </assert_contents> + </output> + </test> +--> + + <!-- Test-5 --> +<!-- + <test> + <section name="req_inputs"> + <conditional name="input_type"> + <param name="input_type_selector" value="2"/> + <param name="input" value="gaactgggcagcagcgatctgaccgcgcgcagcccgtatcgcgaatttaccgatcatctggtgaaa"/> + </conditional> + <param name="db_file" ftype="fasta" value="Uniprot.fasta"/> + <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/> + </section> + <section name="modifications"> + <param name="fixed_mod" value="6,103,157"/> + <param name="var_mod" value="117"/> + <param name="max_mods" value="3"/> + <param name="unmodified" value="False"/> + <param name="aa" value="True"/> + </section> + <section name="ms_params"> + <section name="tolerance_params"> + <param name="precursor_tolerance" value="10"/> + <param name="precursor_unit" value="ppm"/> + <param name="tolerance" value="0.6"/> + </section> + <section name="digestion"> + <param name="enzyme" value="0"/> + <param name="max_missed_cleavages" value="2"/> + </section> + <section name="search"> + <param name="frag_method" value="1"/> + <param name="scoring_method" value="1"/> + <param name="max_charge" value="3"/> + <param name="min_charge" value="2"/> + <param name="min_peaks" value="10"/> + <param name="min_score" value="12"/> + <param name="max_length" value="45"/> + <param name="num_random_peptides" value="1000"/> + </section> + </section> + <output name="psm_rank_txt"> + <assert_contents> + <has_text text="ELGSSDLTAR" /> + </assert_contents> + </output> + </test> +--> + + <!-- Test-6 --> +<!-- + <test> + <section name="req_inputs"> + <conditional name="input_type"> + <param name="input_type_selector" value="peptide"/> + <conditional name="multiple"> + <param name="peptide_input_selector" value="multiple" /> + <param name="input" ftype="tabular" value="novel_peptides"/> + </conditional> + </conditional> + <param name="db_file" ftype="fasta" value="Uniprot.fasta"/> + <param name="spectrum_file" ftype="mgf" value="immunopeptidomics.mgf"/> + <param name="indexType" value="2"/> + <conditional name="tags"> + <param name="tagType" value="PepQuery"/> + <param name="tag_file" ftype="tabular" value="test.tags"/> + <param name="tagIndexType" value="2"/> + </conditional> + </section> + <section name="modifications"> + <param name="fixed_mod" value=""/> + <param name="var_mod" value="117,114,118,128"/> + <param name="max_mods" value="3"/> + <param name="unmodified" value="True"/> + <param name="aa" value="True"/> + </section> + <section name="ms_params"> + <section name="tolerance_params"> + <param name="precursor_tolerance" value="20"/> + <param name="precursor_unit" value="ppm"/> + <param name="tolerance" value="0.02"/> + </section> + <section name="digestion"> + <param name="enzyme" value="0"/> + <param name="max_missed_cleavages" value="0"/> + </section> + <section name="search"> + <param name="frag_method" value="1"/> + <param name="scoring_method" value="1"/> + <param name="max_charge" value="3"/> + <param name="min_charge" value="2"/> + <param name="min_peaks" value="10"/> + <param name="min_score" value="12"/> + <param name="max_length" value="25"/> + <param name="num_random_peptides" value="1000"/> + </section> + </section> + <output name="psm_rank_txt"> + <assert_contents> + <has_text text="MTDRHAGTY" /> + <has_text text="controllerType=0 controllerNumber=1 scan=19905" /> + </assert_contents> + </output> + </test> +--> + + <!-- Test-7 --> +<!-- + <test> + <section name="req_inputs"> + <conditional name="input_type"> + <param name="input_type_selector" value="peptide"/> + <conditional name="multiple"> + <param name="peptide_input_selector" value="multiple" /> + <param name="input" ftype="tabular" value="novel_peptides"/> + </conditional> + </conditional> + <param name="db_file" ftype="fasta" value="Uniprot.fasta"/> + <param name="spectrum_file" ftype="mgf" value="immunopeptidomics.mgf"/> + <param name="indexType" value="2"/> + <conditional name="tags"> + <param name="tagType" value="pFind"/> + <param name="qry_res" ftype="txt" value="pFind.qry.res"/> + </conditional> + </section> + <section name="modifications"> + <param name="fixed_mod" value=""/> + <param name="var_mod" value="117,114,118,128"/> + <param name="max_mods" value="3"/> + <param name="unmodified" value="True"/> + <param name="aa" value="True"/> + </section> + <section name="ms_params"> + <section name="tolerance_params"> + <param name="precursor_tolerance" value="20"/> + <param name="precursor_unit" value="ppm"/> + <param name="tolerance" value="0.02"/> + </section> + <section name="digestion"> + <param name="enzyme" value="0"/> + <param name="max_missed_cleavages" value="0"/> + </section> + <section name="search"> + <param name="frag_method" value="1"/> + <param name="scoring_method" value="1"/> + <param name="max_charge" value="3"/> + <param name="min_charge" value="2"/> + <param name="min_peaks" value="10"/> + <param name="min_score" value="12"/> + <param name="max_length" value="25"/> + <param name="num_random_peptides" value="1000"/> + </section> + </section> + <output name="psm_rank_txt"> + <assert_contents> + <has_text text="MTDRHAGTY" /> + <has_text text="controllerType=0 controllerNumber=1 scan=19905" /> + </assert_contents> + </output> + </test> +--> + + </tests> + <help><![CDATA[ +**PepQuery** + +PepQuery_ is a universal targeted peptide search engine for identifying or validating known and novel peptides of interest in any local or publicly available mass spectrometry-based proteomics datasets. + + +PepQuery_ is a peptide-centric search engine for novel peptide identification and validation. Cancer genomics studies have identified a large number of genomic alterations that may lead to novel, cancer-specific protein sequences. Proteins resulted from these genomic alterations are attractive candidates for cancer biomarkers and therapeutic targets. The leading approach to proteomic validation of genomic alterations is to analyze tandem mass spectrometry (MS/MS) data using customized proteomics databases created from genomics data. Such analysis is time-consuming and requires thorough training and detailed knowledge in proteomics data analysis, leading to a gap between MS/MS data and the cancer genomics community. PepQuery does not require customized databases and allows quick and easy proteomic validation of genomic alterations. + +PepQuery2 leverages a new MS/MS indexing approach and cloud storage to enable ultrafast, targeted identification of both novel and known peptides. PepQuery2 allows users to search more than one billion MS/MS data indexed in the PepQueryDB from any computers with internet access. It also supports direct analysis of user provided MS/MS data, any public datasets in PRIDE, MassIVE, jPOSTrepo and iProX, or Universal Spectrum Identifiers (USIs) from ProteomeXchange. + +**Inputs** + - A sequence to match, one of the following: + + - A peptide string or a history dataset with a list of peptides + - A protein string or a history dataset with a protein fasta + - A DNA string that is at least 60 base pairs in length + + - MS/MS data used for identification: + + - A mass spectrometry history datasets in MGF, mzML, or mzXML format + - An Indexed MS/MS dataset + - PepQueryDB dataset IDs + - Dataset IDs from public proteomics data repositories: PRIDE, MassIVE, jPOSTrepo and iProX + + - A reference protein fasta database, novel peptides matching a reference sequence will be excluded. + + - A protein fasta file + - The ID for a public reference protein database from RefSeq, GENCODE, Ensembl or UniProt. + + +**Outputs** + - Parameters: + + - parameters used in the search + + - PSM - tabular with columns: + + - peptide modification n spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue + + - PSM Rank - tabular with columns: + + - peptide modification n spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue rank *n_ptm* + + - An MGF with the best matching spectrums + + - Detail - tabular with columns: + + - spectrum_title peptide modification pep_mass score + + - PSM annotation - tabular with columns: + + - peptide Query calc_mr observed_mz charge pepSeq m_label m_mz m_intensity mz intensity + + - PTM - tabular with columns: + + - spectrum_title peptide charge exp_mass pep_mass tol_ppm tol_da isotope_error modification score + + - PTM Detail - tabular with columns: + + - peptide modification n spectrum_title charge exp_mass tol_ppm tol_da isotope_error pep_mass mz score n_db total_db n_random total_random pvalue rank ptm_spectrum_title ptm_peptide ptm_charge ptm_exp_mass ptm_pep_mass ptm_tol_ppm ptm_tol_da ptm_isotope_error ptm_modification ptm_score + + - An Indexed MS/MS dataset *when MS/MS data is MGF, mzML, or mzXML history datasets* + + The *n_ptm* field is added when using unrestricted modification searching (-um). + +.. _PepQuery: http://pepquery.org/document.html + + ]]></help> + <expand macro="citations" /> +</tool>