Mercurial > repos > galaxyp > pepquery2_show_sets
changeset 0:b9e1e95758e8 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
| author | galaxyp |
|---|---|
| date | Sun, 06 Nov 2022 16:24:53 +0000 |
| parents | |
| children | 8671cf7c1671 |
| files | macros.xml pepquery2_show_sets.xml test-data/AgilentMassHunterTest.mzXML test-data/Uniprot.fasta test-data/iTRAQ_f4.mgf test-data/immunopeptidomics.mgf test-data/novel_peptides test-data/novel_proteins.fa test-data/pep.txt test-data/small-index-filter.mzML |
| diffstat | 10 files changed, 7416 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun Nov 06 16:24:53 2022 +0000 @@ -0,0 +1,1302 @@ + <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="pepquerydb_options"> + <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> + </xml> + + <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_show_sets.xml Sun Nov 06 16:24:53 2022 +0000 @@ -0,0 +1,86 @@ +<tool id="pepquery2_show_sets" name="PepQuery2 Show Sets" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5"> + <description>PepQueryDB datasets, Parameters, PTMs</description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">pepquery</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ +echo "PepQuery2 Show Sets $sets" +#if 'PepQueryDB_datasets' in $sets + && pepquery -b show_full | sed 's/.*\(NO[.]\)/\1/' | grep '^[N1-9]' | sed 's/[ ][ ]*\$//' | sed 's/[ ][ ]*/\t/g' > '$pepquerydb' +#end if +#if 'parameter_sets' in $sets + && pepquery -p show | grep -v INFO | sed 's/^.\[m//' > $parameters +#end if +#if 'printPTM' in $sets + && pepquery -printPTM | grep -v INFO | sed 's/^.\[m//' > $ptm_list +#end if + ]]></command> + <inputs> + <param name="sets" type="select" multiple="true" optional="false" label="PepQuery Set"> + <option value="PepQueryDB_datasets" selected="true">PepQueryDB Datasets</option> + <option value="parameter_sets">PepQuery Predefined Parameter Sets</option> + <option value="printPTM">PepQuery Modifications</option> + </param> + </inputs> + <outputs> + <data name="pepquerydb" format="tabular" label="PepQueryDB datasets"> + <filter>'PepQueryDB_datasets' in sets</filter> + <actions> + <action name="comment_lines" type="metadata" default="1" /> + <action name="column_names" type="metadata" default="NO.,dataset_name,short_name,parameter_set,species,data_type,n_spectra,n_ms_file,data_link" /> + </actions> + </data> + <data name="parameters" format="txt" label="PepQuery Predefined Parameter Sets"> + <filter>'parameter_sets' in sets</filter> + </data> + <data name="ptm_list" format="tabular" label="PepQuery Modifications"> + <filter>'printPTM' in sets</filter> + <actions> + <action name="comment_lines" type="metadata" default="1" /> + <action name="column_names" type="metadata" default="mod_id,mod_name,mod_mass,mod_type,mod_category,unimod_accession" /> + </actions> + </data> + </outputs> + <tests> + <test> + <output name="pepquerydb"> + <assert_contents> + <has_text text="CPTAC_PDA_Discovery_Study_Proteome_PDC000270" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +**Show available: PepQueryDB Datasets, Parameter Sets, and PTMs** *(Post Translational Modifications)* + +@PEPQUERY_DOCUMANTATION_URL@ + +**PepQueryDB Datasets** + + - Shows a table of all the indexed MS/MS datasets available in PepQueryDB. + - *java -jar pepquery-2.0.2.jar -b show_full* + - These datasets can be used for the **-b** option in **PepQuery**. + - The parameter_set value can be used in the **-p** option in **PepQuery**. + - Columns: NO. dataset_name short_name parameter_set species data_type n_spectra n_ms_file data_link + + +**PepQuery Predefined Parameter Sets** + + - Shows the predefined Parameter Set Names with the option settings + - *java -jar pepquery-2.0.2.jar -p show* + - The parameterset names can be used for the **-p** option in **PepQuery**. + + +**PepQuery Modifications** + + - Shows a table of the PTMs available + - *java -jar pepquery-2.0.2.jar -printPTM* + - The mod_id numbers can be used in the **-fixMOD** and **-varMOD** options in **PepQuery**. + - Columns: mod_id mod_name mod_mass mod_type mod_category unimod_accession + + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AgilentMassHunterTest.mzXML Sun Nov 06 16:24:53 2022 +0000 @@ -0,0 +1,4263 @@ +<?xml version="1.0" encoding="ISO-8859-1"?> +<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2" + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2 http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_idx_3.2.xsd"> + <msRun scanCount="212" startTime="PT0.668S" endTime="PT209.708S"> + <msInstrument msInstrumentID="1"> + <msManufacturer category="msManufacturer" value="instrument model"/> + <msModel category="msModel" value="Agilent instrument model"/> + <msIonisation category="msIonisation" value="microelectrospray"/> + <msMassAnalyzer category="msMassAnalyzer" value="time-of-flight"/> + <msDetector category="msDetector" value="microchannel plate detector"/> + <software type="acquisition" name="MassHunter Data Acquisition" 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Uniprot.fasta Sun Nov 06 16:24:53 2022 +0000 @@ -0,0 +1,20 @@ +>sp|Q8C4J7|TBL3_MOUSE Transducin beta-like protein 3 OS=Mus musculus GN=Tbl3 PE=2 SV=1 +MAETAAGLCRFKANYAVERKIEPFYKGGKAQLDQTGHYLFCVCGTKVNILDVASGALLRSLEQEDQEDITSFDLSPDDEVLVTASRALLLAQWAWREGTVTRLWKAIHTAPVASMAFDATSTLLATGGCDGAVRVWDIVQHYGTHHFRGSPGVVHLVAFHPDPTRLLLFSSAVDTSIRVWSLQDRSCLAVLTAHYSAVTSLSFSEGGHTMLSSGRDKICIVWDLQSYQTTRTVPVFESVEASVLLPEQPAPALGVKSSGLHFLTAGDQGILRVWEAASGQCVYTQPQMPGLRQELTHCTLARAADLLLTVTADHNLLLYEAHSLQLQKQFAGYSEEVLDVRFLGPSDSHIVVASNSPCLKVFELQTLACQILHGHTDIVLALDVFRKGWLFASCAKDQSIRIWKMNKAGQVACVAQGSGHTHSVGTICCSRLKESFLVTGSQDCTVKLWPLPEALLAKSTAADSGPVLLQAQTTRRCHDKDINSLAVSPNDKLLATGSQDRTAKLWALPQCQLLGVFTGHRRGLWNVQFSPTDQVLATASADGTIKLWALQDFSCLKTFEGHDASVLKVAFVSRGSQLLSSGSDGLLKLWTIKSNECVRTLDAHEDKVWGLHCSQLDDHAITGGSDSRIILWKDVTEAEQAEEQAKREEQVIKQQELDNLLHEKRYLRALGLAISLDRPHTVLTVIQAIRRDPEACEKLEATVLRLRRDQKEALLRFCVTWNTNSRHCHEAQAVLGVLLRHEAPEELLAYDGVRGSLEALLPYTERHFQRLSRTLQAATFLDFLWHNMKLSPCPAAAPPAL +>tr|Q80ZP8|Q80ZP8_MOUSE Armet protein OS=Mus musculus GN=Manf PE=1 SV=1 +METNNYLPSPPSFPVCISYLGRFYQDLKDRDVTFSPATIEEELIKFCREARGKENRLCYYIGATDDAATKIINEVSKPLAHHIPVEKICEKLKKKDSQICELKYDKQIDLSTVDLKKLRVKELKKILDDWGEMCKGCAEKSDYIRKINELMPKYAPKAASARTDL +>sp|Q60847|COCA1_MOUSE Collagen alpha-1(XII) chain OS=Mus musculus GN=Col12a1 PE=2 SV=3 +MQTRLPRALAALGVALLLSSIEAEVDPPSDLNFKIIDENTVHMSWERPVDPIVGYRITVDPTTDGPTKEFTLAASTTETLLSDLIPETQYVVTITSYNEVEESVPVIGQLTIQTGGPTKPGEKKPGKTEIQKCSVSAWTDLVFLVDGSWSVGRNNFKYILDFIVALVSAFDIGEEKTRVGVVQYSSDTRTEFNLNQYYRREDLLAAVKKIPYKGGNTMTGDAIDYLVKNTFTESAGSRAGFPKVAIIITDGKSQDEVEIPARELRNIGVEVFSLGIKAADAKELKQIASTPSLNHVFNVANFDAIVDIQNEIISQVCSGVDEQLGELVSGEEVIEPPSNLVVTELSSKYIRLSWDPSPSAVTGYKILLTPMAAGSRHHALSVGPQTTTLNVRDLTADTEYQISVFAMKGLTSSEPTSVMEKTQPMKVQVECSRGVDIKADIVFLVDGSYSIGIANFVKVRAFLEVLAKSFEISPNRVQISLVQYSRDPHTEFTLKEFNRVEDIIKAINTFPYRGGSTNTGKAMTYVREKIFVPNKGSRSNVPKVMILITDGKSSDAFRDPAIKLRNSDVEIFAVGVKDAVRSELEAIASPPAETHVFTVEDFDAFQRISFELTQSICLRIEQELAAIKKKAYVPPKDLRFTQVTANSFKAEWSPPGDNVFSYHVTYKDANGDDEVTVVEPASSTSVVLNNLRPETLYLVNVTAEYEDGFSVPITGEETTAEVKGVPRNLKVTDETTDSFKLTWSQAPGRVLRYRIRYRPVSGGESKEVSTPANQRRKTLENLTPDTKYEISVIAEYSSGPGSPLTGNAATEEVRGNPRDLRVSDATTSTLKLSWSRAPGKVKQYLVTYTPAAGGETQEVTVRGDTTTTMLRKLKEGTQYDLSVTALYASGAGEALSGKGSTLEERGSPQNLVTKDITDTSIGAYWTSAPGMVRGYRVSWKSLYDDIEAGETTLPGDAIHTMIENLQPETKYKISVFATYSSGEGEPVTGDATTELSQDSKILRVDEETEHTMRVTWKAAPGKVVNYRVVYRPQGGGRQMVAKVPPTVTSTVLKRLQPQTTYDITVLPMYKTGEGKLRQGSGTTASRFKSPRNLKTSDPTMSSFRVTWEPAPGEVKGYKVTFHPTGDDRRLGELVLGPYDNTVVLEELRAGTTYRVNVFGMFDGGESLPLVGQEMTTLSDTTVTPFLSSGMDCLTRAEADIVLLVDGSWSIGRANFRTVRSFISRIVEVFEIGPKRVQIALAQYSGDPRTEWQLNAHRDKKSLLQAVANLPYKGGNTLTGMALNFIRQQSFKTQAGMRPRARKIGVLITDGKSQDDVEAPSKKLKDEGVELFAIGIKNADEVELKMIATDPDDTHAYNVADFESLSKIVDDLTINLCNSVKGPGDLEAPTNLVISERTHRSFRVSWTPPSDSVDRYKVEYYPVSGGKRQEFYVSRLDTSTVLKDLKPETDYVVNVYSVVEDEYSEPLKGTEKTLPVPVVSLNIYDVGPTTMHVQWQPVGGATGYTVSYQPTRSPEGTKPKEMRVGPTVNDVQLTGLLPNTEYEVTVQAVLYDLTSEPAKAREVTLPLPRPQDVKLRDVTHSTMNVVWEPVLGKVRKYIVRYKTPDEEFKEVEVDRSRASTILKDLSSQTQYTVSVSAVYDEGTSPPATAYDTTRRVPAPTNLQFTEVTPESFRGTWDHGASDVSLYRITWAPVGNPDKMETILNGDENTLVFENLNPNTPYEVSITAIYPDESESEDLSGTERTLRLIPLTTQAPKSGPRNLQVYNATSNSLTVKWDPASGRVQKYRITYQPSTGEGNEQTITVGGRQNSVLLQKLKPDTPYTITVYSQYPDGEGGRMTGRGKTKPLNTVRNLRVYDPSTSSLSVRWDHAEGNPRQYKLFYAPTSGGPEELVPIPGNTNYAILRNLQPDTPYTITVVPVYTEGDGGRTSDTGRTLVRGLARNIQVYNPTPNSLDVRWDPAPGPVQQYRIVYSPVAGTRPSESIVVPGNTRTVHLERLIPDTPYSVNIVALYSDGEGNPSPSQGRTLPRSGPRNIRVFGETTNSLSVAWDHADGPVQQYRIIYSPTVGDPIDEYTTVPGRRNNVILQPLQPDTPYKITVIAIYEDGDGGHLTGNGRTVGLLPPQNIHIFDEWYTRFRVSWDPSPSPVLGYKIVYKPVGSNEPMEAFVGEVTSYTLHNLNPSTTYDVSVYAQYDSGLSVPLTDQGTTLYLNVTDLKTYQVGWDTFCVKWSPHRAATSYRLKLSPADGTRGQEITVRGSETSHCFTGLSPEAEYGVTVFVQTPNLEGPGVPIKEQTTVKPTEAPTEPPTPSPPPTIPPARDVCKGAKADIVFLTDASWSIGDDNFNKVVKFIFNTVGAFDEVNPAGIQVSFVQYSDEVKSEFKLNTYNDKALALGALQNIRYRGGNTRTGKALTFIKEKVLTWESGMRKNVPKVLVVVTDGRSQDEVKKAAFVIQQSGFSVFVVGVADVDYNELANIASKPSERHVFIVDDFESFEKIEDNLITFVCETATSSCPLIYLDGYTSPGFKMLEAYNLTEKNFASVQGVSLESGSFPSYSAYRLQKNAFINQPTAELHPNGLPPSYTIILLFRLLPETPSDPFAIWQITDRDYRPQVGVIADPSSKTLSFFNKDTRGEVQTVTFDTDEVKTLFYGSFHKVHIVVTSKSVKIYIDCYEIIEKDIKEAGNITTDGYEILGKLLKGERKSATFQIQSFDIVCSPVWTSRDRCCDIPSRRDEAKCPALPNACTCTQDSVGPPGPPGPAGGPGAKGPRGERGINGAVGPPGPRGDTGPPGPQGPPGPQGPNGLSIPGEQGRQGMKGDAGEPGLPGRTGTPGLPGPPGPMGPPGDRGFTGKDGAMGPRGPPGPPGSPGSPGVTGPSGKPGKPGDHGRPGQSGLKGEKGDRGDIASQNMMRAVARQVCEQLISGQMSRFNQMLNQIPNDYHSSRNQPGPPGPPGPPGSAGARGEPGPGGRPGFPGTPGMQGPPGERGLPGEKGERGTGSQGPRGPPGPPGPQGESRTGPPGSTGSRGPPGPPGRPGNSGIRGPPGPPGYCDSSQCASIPYNGQGYPEPYVPEGGAYLPEREPFIVPVEPERTAEYEDDYGADEPDQQHPDHMRWRRALRPGPAE +>tr|D6RFR8|D6RFR8_MOUSE Choline/ethanolaminephosphotransferase 1 OS=Mus musculus GN=Cept1 PE=4 SV=1 +MSGHRSTRKRCGDSHPESPVGFGHMSTTGHLCGLILPVLVAFSFTSLWMP +>tr|Q91VK2|Q91VK2_MOUSE Eef1d protein OS=Mus musculus GN=Eef1d PE=1 SV=1 +MATNFLAHEKIWFDKFKYDDAERRFYEQMNGPVTSGSRQLKVMLPNSPEALGQATPGTSSGPGASSGPGGDHSELIVRITSLEVENQNLRGVVQDLQQAISKLEARLSSLEKSSPTPRATAPQTQHVSPMRQVEPPTKKGATPAEDDEDKDIDLFGSDEEEEDKEAARLREERLRQYAEKKAKKPTLVAKSSILLDVKPWDDETDMAQLETCVRSIQLDGLVWGASKLVPVGYGIRKLQIQCVVEDDKVGTDLLEEEITKFEEHVQSVDIAAFNKI +>tr|F6WN43|F6WN43_MOUSE Iron-sulfur cluster co-chaperone protein HscB, mitochondrial (Fragment) OS=Mus musculus GN=Hscb PE=1 SV=1 +XQKSQTEKHFSDKHSTLVNDAYKTLQAPLTRGLYLVS +>sp|Q6NXK2|ZN532_MOUSE Zinc finger protein 532 OS=Mus musculus GN=Znf532 PE=1 SV=1 +MTMGDMKTPDFDDLLAAFDIPDMVDPKAAIESGHDDHESHIKQNAHVDDDSHTPSSSDVGVSVIVKNVRNIDSSEGVEKDGHNPTGNGLHNGFLTASSLDSYGKDGAKSLKGDTPASEVTLKDPAFSQFSPISSAEEFEDDEKIEVDDPPDKEEARAGFRSNVLTGSAPQQDFDKLKALGGENSSKTGVSTSGHTDKNKVKREAESNSITLSVYEPFKVRKAEDKLKENSEKMLESRVLDGKPSSEKSDSGIAAAASSKTKPSSKLSSCIAAIAALSAKKAASDSCKEPVANSREASPLPKEVNDSPKAADKSPESQNLIDGTKKASLKPSDSPRSVSSENSSKGSPSSPVGSTPAIPKVRIKTIKTSSGEIKRTVTRVLPEVDLDSGKKPSEQAASVMASVTSLLSSSASATVLSSPPRAPLQTAMVTSAVSSAELTPKQVTIKPVATAFLPVSAVKTAGSQVINLKLANNTTVKATVISAASVQSASSAIIKAANAIQQQTVVVPASSLANAKLVPKTVHLANLNLLPQGAQATSELRQVLTKPQQQIKQAIINAAASQPPKKVSRVQVVSSLQSSVVEAFNKVLSSVNPVPVYTPNLSPPANAGITLPMRGYKCLECGDAFALEKSLSQHYDRRSVRIEVTCNHCTKNLVFYNKCSLLSHARGHKEKGVVMQCSHLILKPVPADQMIVPPSSNTAASTLQSSVGAATHTVPKVQPGIAGAVISAPASTPMSPAMPLDEDPSKLCRHSLKCLECNEVFQDEPSLATHFQHAADTSGQQMKKHPCRQCDKSFSSSHSLCRHNRIKHKGIRKVYACSHCPDSRRTFTKRLMLERHIQLMHGIKDPDVKELSDDAGDVTNDEEEEAEIKEDAKVPSPKRKLEEPVLEFRPPRGAITQPLKKLKINVFKVHKCAVCGFTTENLLQFHEHIPQHRSDGSSHQCRECGLCYTSHGSLARHLFIVHKLKEPQPVSKQNGAGEDSQQENKPSPEDEAAEGAASDRKCKVCAKTFETEAALNTHMRTHGMAFIKSKRMSSAEK +>sp|P58006|SESN1_MOUSE Sestrin-1 OS=Mus musculus GN=Sesn1 PE=1 SV=3 +MRLAAASNEAYAASLAVSELLSCHQCGGDRGQDEELGIRIPRPLGHGPSRFIPEKEMLQVGSEDAQMHALFADSFAALGRLDNITLVMVFHPQYLESFLKTQHYLLQMDGPLPLHYRHYIGIMAAARHQCSYLVNLHVSDFLHVGGDPKWLNGLENAPQKLQNLGELNKVLAHRPWLITKEHIEGLLKAEEHSWSLAELVHAVVLLTHYHSLASFTFGCGISPEIHCDGGHTFRPPSVSNYCICDITNGNHSVDEMQVNSAGNASVSDSFFEVEALMEKMRQLQECREEEEASQEEMASRFEMEKRESMFVFSSDDDEVTPARDVSRHFEDTSYGYKDFSRHGMHVPTFRVQDYCWEDHGYSLVNRLYPDVGQLIDEKFHIAYNLTYNTMAMHKDVDTSMLRRAIWNYIHCMFGIRYDDYDYGEINQLLDRSFKVYIKTVVCTPEKVTKRMYDSFWRQFKHSEKVHVNLLLIEARMQAELLYALRAITRYMT +>tr|A0A1B0GSE5|A0A1B0GSE5_MOUSE Ubiquitin carboxyl-terminal hydrolase CYLD OS=Mus musculus GN=Cyld PE=1 SV=1 +MSSGLWSQEKVTSPYWEERIFYLLLQECSVTDKQTQKLLKVPKGSIGQYIQDRSVGHSRVPSTKGKKNQIGLKILEQPHAVLFVDEKDVVEINEKFTELLLAITNCEERLSLFRNRLRLSKGLQVDVGSPVKVQLRSGEEKFPGVVRFRGPLLAERTVSGIFFGVELLEEGRGQGFTDGVYQGKQLFQCDEDCGVFVALDKLELIEDDDNGLESDFAGPGDTMQVEPPPLEINSRVSLKVGESTESGTVIFCDVLPGKESLGYFVGVDMDNPIGNWDGRFDGVQLCSFASVESTILLHINDIIPDSVTQERRPPKLAFMSRGVGDKGSSSHNKPKVTGSTSDPGSRNRSELFYTLNGSSVDSQQSKSKNPWYIDEAFGGYLSEVVEENTPPKMEKEGLEIMIGKKKGIQGHYNSCYLDSTLFCLFAFSSALDTVLLRPKEKNDIEYYSETQELLRTEIVNPLRIYGYVCATKIMKLRKILEKVEAASGFTSEEKDPEEFLNILFHDILRVEPLLKIRSAGQKVQDCNFYQIFMEKNEKVGVPTIQQLLEWSFINSNLKFAEAPSCLIIQMPRFGKDFKLFKKIFPSLELNITDLLEDTPRQCRICGGLAMYECRECYDDPDISAGKIKQFCKTCSTQVHLHPRRLNHSYHPVSLPKDLPDWDWRHGCIPCQKMELFAVLCIETSHYVAFVKYGKDDSAWLFFDSMADRDGGQNGFNIPQVTPCPEVGEYLKMSLEDLHSLDSRRIQGCARRLLCDAYMCMYQSPTMSLYK +>sp|Q60880|OL141_MOUSE Olfactory receptor 141 OS=Mus musculus GN=Olfr141 PE=3 SV=2 +MRNITEATFFVLKGLTDNNELQIILFLLFLAIYIFTLIGNVGLIILVVGDSQLHNPMYCFLSVLSSVDACYSTDITPNMLVGFMSKSKIISFYGCATQMFLAVTFGTTECFLLAAMAYDRYVAIHDPLLYAVSMSPRVYIPLIIASYAGGIVHAIIHTVATFSLSFCRSNEVKHIFCDIPPLLAISCSETYVNELLLFFFVSFIELVTILIVLVSYAFILLSILKMNSSEGRRKVFSTCGAHLTAVSIYYGTILFMYVRPSSNYSLEHDMIVSTFYTIGIPMLNPIIYSLRNKDVKEAMKRVLRKKINIKHRIKKLNDFSVFLMP
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/iTRAQ_f4.mgf Sun Nov 06 16:24:53 2022 +0000 @@ -0,0 +1,753 @@ +COM=Conversion to mascot generic +CHARGE=2+ and 3+ +BEGIN IONS +PEPMASS=740.462952 +CHARGE=3+ +SCANS=277 +TITLE=Mo_Tai_iTRAQ_f4.00277.00277.3 +111.017494 85.198502 +112.240982 97.204994 +114.110542 168.274780 +115.107582 369.265503 +115.650398 84.005325 +117.296082 86.641182 +117.595589 82.974037 +120.657990 81.247025 +123.208023 88.939392 +126.714996 76.470490 +126.995316 81.651260 +129.369080 82.580246 +129.410400 90.817963 +132.734039 124.614685 +143.307465 87.847046 +178.966888 94.961578 +179.972855 89.878273 +183.256714 104.533241 +188.080093 123.015953 +212.102753 442.314178 +213.104324 84.621696 +233.001801 107.842552 +244.242355 102.163200 +281.079132 97.696259 +291.216034 243.588058 +309.183807 104.681831 +325.188324 282.187622 +345.226288 167.099777 +347.629883 88.744476 +357.377533 105.747673 +388.266266 1321.324341 +430.317047 94.113419 +458.310547 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