RubyGems - mspire-mascot-dat - Versions diffs - 0.0.1 - Mend

mspire-mascot-dat 0.0.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (23) hide show

data/.document +5 -0
data/.rspec +1 -0
data/LICENSE.txt +21 -0
data/README.md +46 -0
data/Rakefile +39 -0
data/VERSION +1 -0
data/lib/mspire/mascot/dat/index.rb +93 -0
data/lib/mspire/mascot/dat/peptide.rb +95 -0
data/lib/mspire/mascot/dat/query.rb +69 -0
data/lib/mspire/mascot/dat.rb +59 -0
data/mspire-mascot-dat.gemspec +70 -0
data/spec/mspire/mascot/dat/index_spec.rb +44 -0
data/spec/mspire/mascot/dat/peptide_spec.rb +24 -0
data/spec/mspire/mascot/dat/query_spec.rb +33 -0
data/spec/mspire/mascot/dat_spec.rb +94 -0
data/spec/reference/dat_format_reference.md +667 -0
data/spec/reference/two_spectra_decoy_F004129.png +0 -0
data/spec/reference/two_spectra_no_decoy_F004128.png +0 -0
data/spec/spec_helper.rb +11 -0
data/spec/testfiles/F004128.dat +897 -0
data/spec/testfiles/F004129.dat +1259 -0
data/spec/testfiles/two_spectra.mgf +864 -0
metadata +133 -0

data/spec/testfiles/F004128.dat ADDED Viewed

@@ -0,0 +1,897 @@
+MIME-Version: 1.0 (Generated by Mascot version 1.0)
+Content-Type: multipart/mixed; boundary=gc0p4Jq0M2Yt08jU534c0p
+--gc0p4Jq0M2Yt08jU534c0p
+Content-Type: application/x-Mascot; name="parameters"
+LICENSE=Licensed to: Brigham Young University, Provo, United States RCCZ-D4GH-S53W-2G5F-NG5L, (1 processor).
+MP=
+NM=
+COM=My Example Search Title Searching Two Spectra NO DECOY
+IATOL=
+IA2TOL=
+IASTOL=
+IBTOL=
+IB2TOL=
+IBSTOL=
+IYTOL=
+IY2TOL=
+IYSTOL=
+SEG=
+SEGT=
+SEGTU=
+LTOL=
+TOL=1.2
+TOLU=Da
+ITH=
+ITOL=0.6
+ITOLU=Da
+PFA=1
+DB=GbetaCCT_drome
+MODS=Carbamidomethyl (C)
+MASS=Monoisotopic
+CLE=Trypsin
+FILE=two_spectra.mgf
+PEAK=AUTO
+QUE=
+TWO=
+SEARCH=MIS
+USERNAME=John T. Doe
+USEREMAIL=myexample@gmail.com
+CHARGE=2+
+INTERMEDIATE=
+REPORT=AUTO
+OVERVIEW=
+FORMAT=Mascot generic
+FORMVER=1.01
+FRAG=
+IT_MODS=Oxidation (M)
+USER00=
+USER01=
+USER02=
+USER03=
+USER04=
+USER05=
+USER06=
+USER07=
+USER08=
+USER09=
+USER10=
+USER11=
+USER12=
+PRECURSOR=
+TAXONOMY=All entries
+ACCESSION=
+REPTYPE=peptide
+SUBCLUSTER=
+ICAT=
+INSTRUMENT=ESI-TRAP
+ERRORTOLERANT=
+FRAMES=
+CUTOUT=
+USERID=0
+QUANTITATION=None
+DECOY=
+PEP_ISOTOPE_ERROR=0
+RULES=1,2,8,9,10,13,14,15
+INTERNALS=0.0,700.0
+--gc0p4Jq0M2Yt08jU534c0p
+Content-Type: application/x-Mascot; name="masses"
+A=71.037114
+B=114.534940
+C=160.030649
+D=115.026943
+E=129.042593
+F=147.068414
+G=57.021464
+H=137.058912
+I=113.084064
+J=0.000000
+K=128.094963
+L=113.084064
+M=131.040485
+N=114.042927
+O=0.000000
+P=97.052764
+Q=128.058578
+R=156.101111
+S=87.032028
+T=101.047679
+U=150.953630
+V=99.068414
+W=186.079313
+X=111.000000
+Y=163.063329
+Z=128.550590
+Hydrogen=1.007825
+Carbon=12.000000
+Nitrogen=14.003074
+Oxygen=15.994915
+Electron=0.000549
+C_term=17.002740
+N_term=1.007825
+delta1=15.994915,Oxidation (M)
+NeutralLoss1=0.000000
+NeutralLoss1_master=63.998285
+FixedMod1=57.021464,Carbamidomethyl (C)
+FixedModResidues1=C
+--gc0p4Jq0M2Yt08jU534c0p
+Content-Type: application/x-Mascot; name="unimod"
+<?xml version="1.0" encoding="UTF-8" ?>
+<umod:unimod xmlns:umod="http://www.unimod.org/xmlns/schema/unimod_2" majorVersion="2" minorVersion="0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.unimod.org/xmlns/schema/unimod_2 unimod_2.xsd">
+  <umod:elements>
+    <umod:elem avge_mass="1.00794" full_name="Hydrogen" mono_mass="1.007825035" title="H"/>
+    <umod:elem avge_mass="2.014101779" full_name="Deuterium" mono_mass="2.014101779" title="2H"/>
+    <umod:elem avge_mass="6.941" full_name="Lithium" mono_mass="7.016003" title="Li"/>
+    <umod:elem avge_mass="12.0107" full_name="Carbon" mono_mass="12" title="C"/>
+    <umod:elem avge_mass="13.00335483" full_name="Carbon13" mono_mass="13.00335483" title="13C"/>
+    <umod:elem avge_mass="14.0067" full_name="Nitrogen" mono_mass="14.003074" title="N"/>
+    <umod:elem avge_mass="15.00010897" full_name="Nitrogen15" mono_mass="15.00010897" title="15N"/>
+    <umod:elem avge_mass="15.9994" full_name="Oxygen" mono_mass="15.99491463" title="O"/>
+    <umod:elem avge_mass="17.9991603" full_name="Oxygen18" mono_mass="17.9991603" title="18O"/>
+    <umod:elem avge_mass="18.9984032" full_name="Fluorine" mono_mass="18.99840322" title="F"/>
+    <umod:elem avge_mass="22.98977" full_name="Sodium" mono_mass="22.9897677" title="Na"/>
+    <umod:elem avge_mass="30.973761" full_name="Phosphorous" mono_mass="30.973762" title="P"/>
+    <umod:elem avge_mass="32.065" full_name="Sulfur" mono_mass="31.9720707" title="S"/>
+    <umod:elem avge_mass="35.453" full_name="Chlorine" mono_mass="34.96885272" title="Cl"/>
+    <umod:elem avge_mass="39.0983" full_name="Potassium" mono_mass="38.9637074" title="K"/>
+    <umod:elem avge_mass="40.078" full_name="Calcium" mono_mass="39.9625906" title="Ca"/>
+    <umod:elem avge_mass="55.845" full_name="Iron" mono_mass="55.9349393" title="Fe"/>
+    <umod:elem avge_mass="58.6934" full_name="Nickel" mono_mass="57.9353462" title="Ni"/>
+    <umod:elem avge_mass="65.409" full_name="Zinc" mono_mass="63.9291448" title="Zn"/>
+    <umod:elem avge_mass="78.96" full_name="Selenium" mono_mass="79.9165196" title="Se"/>
+    <umod:elem avge_mass="79.904" full_name="Bromine" mono_mass="78.9183361" title="Br"/>
+    <umod:elem avge_mass="107.8682" full_name="Silver" mono_mass="106.905092" title="Ag"/>
+    <umod:elem avge_mass="200.59" full_name="Mercury" mono_mass="201.970617" title="Hg"/>
+    <umod:elem avge_mass="196.96655" full_name="Gold" mono_mass="196.966543" title="Au"/>
+    <umod:elem avge_mass="126.90447" full_name="Iodine" mono_mass="126.904473" title="I"/>
+    <umod:elem avge_mass="95.94" full_name="Molybdenum" mono_mass="97.9054073" title="Mo"/>
+    <umod:elem avge_mass="63.546" full_name="Copper" mono_mass="62.9295989" title="Cu"/>
+    <umod:elem avge_mass="0.000549" full_name="electron" mono_mass="0.000549" title="e"/>
+    <umod:elem avge_mass="10.811" full_name="Boron" mono_mass="11.0093055" title="B"/>
+    <umod:elem avge_mass="74.9215942" full_name="Arsenic" mono_mass="74.9215942" title="As"/>
+    <umod:elem avge_mass="112.411" full_name="Cadmium" mono_mass="113.903357" title="Cd"/>
+    <umod:elem avge_mass="51.9961" full_name="Chromium" mono_mass="51.9405098" title="Cr"/>
+    <umod:elem avge_mass="58.933195" full_name="Cobalt" mono_mass="58.9331976" title="Co"/>
+    <umod:elem avge_mass="54.938045" full_name="Manganese" mono_mass="54.9380471" title="Mn"/>
+    <umod:elem avge_mass="24.305" full_name="Magnesium" mono_mass="23.9850423" title="Mg"/>
+    <umod:elem avge_mass="69.723" full_name="Gallium" mono_mass="68.9255736" title="Ga"/>
+  </umod:elements>
+  <umod:modifications>
+    <umod:mod approved="true" date_time_modified="2006-10-16 10:18:27" date_time_posted="2002-08-19 19:17:11" full_name="Iodoacetamide derivative" group_of_poster="admin" record_id="4" title="Carbamidomethyl" username_of_poster="unimod">
+      <umod:specificity classification="Artefact" hidden="true" position="Anywhere" site="D" spec_group="5"/>
+      <umod:specificity classification="Artefact" hidden="true" position="Anywhere" site="H" spec_group="4"/>
+      <umod:specificity classification="Artefact" hidden="true" position="Any N-term" site="N-term" spec_group="3"/>
+      <umod:specificity classification="Artefact" hidden="true" position="Anywhere" site="K" spec_group="2"/>
+      <umod:specificity classification="Chemical derivative" hidden="false" position="Anywhere" site="C" spec_group="1"/>
+      <umod:specificity classification="Artefact" hidden="true" position="Anywhere" site="E" spec_group="6"/>
+      <umod:delta avge_mass="57.0513" composition="H(3) C(2) N O" mono_mass="57.021464">
+        <umod:element number="3" symbol="H"/>
+        <umod:element number="2" symbol="C"/>
+        <umod:element number="1" symbol="N"/>
+        <umod:element number="1" symbol="O"/>
+      </umod:delta>
+      <umod:alt_name>Carboxyamidomethylation</umod:alt_name>
+      <umod:xref>
+        <umod:text>Creasy, D. M., Cottrell, J. S., Proteomics 2 1426-34 (2002)</umod:text>
+        <umod:source>Journal</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>11510821</umod:text>
+        <umod:source>PubMed PMID</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>Boja, E. S., Fales, H. M., Anal. Chem. 73 3576-82 (2001)</umod:text>
+        <umod:source>Journal</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>12422359</umod:text>
+        <umod:source>PubMed PMID</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+    </umod:mod>
+    <umod:mod approved="false" date_time_modified="2008-02-15 05:37:07" date_time_posted="2002-08-19 19:17:11" full_name="Oxidation or Hydroxylation" group_of_poster="admin" record_id="35" title="Oxidation" username_of_poster="unimod">
+      <umod:specificity classification="Artefact" hidden="false" position="Anywhere" site="W" spec_group="10"/>
+      <umod:specificity classification="Artefact" hidden="false" position="Anywhere" site="H" spec_group="10"/>
+      <umod:specificity classification="Post-translational" hidden="true" position="Anywhere" site="C" spec_group="9">
+        <umod:misc_notes>Cysteine sulfenic acid</umod:misc_notes>
+      </umod:specificity>
+      <umod:specificity classification="Artefact" hidden="false" position="Anywhere" site="M" spec_group="8">
+        <umod:NeutralLoss avge_mass="0.0000" composition="0" flag="false" mono_mass="0.000000"/>
+        <umod:NeutralLoss avge_mass="64.1069" composition="H(4) C O S" flag="false" mono_mass="63.998285">
+          <umod:element number="4" symbol="H"/>
+          <umod:element number="1" symbol="C"/>
+          <umod:element number="1" symbol="O"/>
+          <umod:element number="1" symbol="S"/>
+        </umod:NeutralLoss>
+      </umod:specificity>
+      <umod:specificity classification="Post-translational" hidden="true" position="Anywhere" site="R" spec_group="7"/>
+      <umod:specificity classification="Post-translational" hidden="true" position="Anywhere" site="Y" spec_group="6"/>
+      <umod:specificity classification="Artefact" hidden="true" position="Anywhere" site="F" spec_group="5"/>
+      <umod:specificity classification="Post-translational" hidden="true" position="Anywhere" site="P" spec_group="4">
+        <umod:misc_notes>Proline oxidation to glutamic semialdehyde</umod:misc_notes>
+      </umod:specificity>
+      <umod:specificity classification="Post-translational" hidden="true" position="Anywhere" site="N" spec_group="3"/>
+      <umod:specificity classification="Post-translational" hidden="true" position="Anywhere" site="K" spec_group="2"/>
+      <umod:specificity classification="Post-translational" hidden="true" position="Anywhere" site="D" spec_group="1"/>
+      <umod:specificity classification="Pre-translational" hidden="true" position="Any C-term" site="G" spec_group="11">
+        <umod:misc_notes>Hydroxyglycine derivative in amidation pathway</umod:misc_notes>
+      </umod:specificity>
+      <umod:delta avge_mass="15.9994" composition="O" mono_mass="15.994915">
+        <umod:element number="1" symbol="O"/>
+      </umod:delta>
+      <umod:xref>
+        <umod:text>HYDR</umod:text>
+        <umod:source>FindMod</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>AA0322</umod:text>
+        <umod:source>RESID</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>11212008</umod:text>
+        <umod:source>PubMed PMID</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>11120890</umod:text>
+        <umod:source>PubMed PMID</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>DOPA</umod:text>
+        <umod:source>FindMod</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>CSEA</umod:text>
+        <umod:source>FindMod</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>14661084</umod:text>
+        <umod:source>PubMed PMID</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>AA0026</umod:text>
+        <umod:source>RESID</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.</umod:text>
+        <umod:source>Journal</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>15569593</umod:text>
+        <umod:source>PubMed PMID</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>AA0205</umod:text>
+        <umod:source>RESID</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>AA0215</umod:text>
+        <umod:source>RESID</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>Lagerwerf FM, van de Weert M, Heerma W, Haverkamp J, Rapid Commun Mass Spectrom. 1996;10(15):1905-10</umod:text>
+        <umod:source>Journal</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>AA0029</umod:text>
+        <umod:source>RESID</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>AA0030</umod:text>
+        <umod:source>RESID</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>9004526</umod:text>
+        <umod:source>PubMed PMID</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>AA0028</umod:text>
+        <umod:source>RESID</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>11461766</umod:text>
+        <umod:source>PubMed PMID</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>AA0027</umod:text>
+        <umod:source>RESID</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>AA0235</umod:text>
+        <umod:source>RESID</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>AA0146</umod:text>
+        <umod:source>RESID</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>14661085</umod:text>
+        <umod:source>PubMed PMID</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>12781462</umod:text>
+        <umod:source>PubMed PMID</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+      <umod:xref>
+        <umod:text>2057999</umod:text>
+        <umod:source>PubMed PMID</umod:source>
+        <umod:url></umod:url>
+      </umod:xref>
+    </umod:mod>
+  </umod:modifications>
+  <umod:amino_acids>
+    <umod:aa avge_mass="0.0000" full_name="" mono_mass="0.000000" three_letter="" title="-"/>
+    <umod:aa avge_mass="71.0779" full_name="Alanine" mono_mass="71.037114" three_letter="Ala" title="A">
+      <umod:element number="5" symbol="H"/>
+      <umod:element number="3" symbol="C"/>
+      <umod:element number="1" symbol="N"/>
+      <umod:element number="1" symbol="O"/>
+    </umod:aa>
+    <umod:aa avge_mass="156.1857" full_name="Arginine" mono_mass="156.101111" three_letter="Arg" title="R">
+      <umod:element number="12" symbol="H"/>
+      <umod:element number="6" symbol="C"/>
+      <umod:element number="4" symbol="N"/>
+      <umod:element number="1" symbol="O"/>
+    </umod:aa>
+    <umod:aa avge_mass="114.1026" full_name="Asparagine" mono_mass="114.042927" three_letter="Asn" title="N">
+      <umod:element number="6" symbol="H"/>
+      <umod:element number="4" symbol="C"/>
+      <umod:element number="2" symbol="N"/>
+      <umod:element number="2" symbol="O"/>
+    </umod:aa>
+    <umod:aa avge_mass="115.0874" full_name="Aspartic acid" mono_mass="115.026943" three_letter="Asp" title="D">
+      <umod:element number="5" symbol="H"/>
+      <umod:element number="4" symbol="C"/>
+      <umod:element number="1" symbol="N"/>
+      <umod:element number="3" symbol="O"/>
+    </umod:aa>
+    <umod:aa avge_mass="103.1429" full_name="Cysteine" mono_mass="103.009185" three_letter="Cys" title="C">
+      <umod:element number="5" symbol="H"/>
+      <umod:element number="3" symbol="C"/>
+      <umod:element number="1" symbol="N"/>
+      <umod:element number="1" symbol="O"/>
+      <umod:element number="1" symbol="S"/>
+    </umod:aa>
+    <umod:aa avge_mass="129.1140" full_name="Glutamic acid" mono_mass="129.042593" three_letter="Glu" title="E">
+      <umod:element number="7" symbol="H"/>
+      <umod:element number="5" symbol="C"/>
+      <umod:element number="1" symbol="N"/>
+      <umod:element number="3" symbol="O"/>
+    </umod:aa>
+    <umod:aa avge_mass="128.1292" full_name="Glutamine" mono_mass="128.058578" three_letter="Gln" title="Q">
+      <umod:element number="8" symbol="H"/>
+      <umod:element number="5" symbol="C"/>
+      <umod:element number="2" symbol="N"/>
+      <umod:element number="2" symbol="O"/>
+    </umod:aa>
+    <umod:aa avge_mass="57.0513" full_name="Glycine" mono_mass="57.021464" three_letter="Gly" title="G">
+      <umod:element number="3" symbol="H"/>
+      <umod:element number="2" symbol="C"/>
+      <umod:element number="1" symbol="N"/>
+      <umod:element number="1" symbol="O"/>
+    </umod:aa>
+    <umod:aa avge_mass="137.1393" full_name="Histidine" mono_mass="137.058912" three_letter="His" title="H">
+      <umod:element number="7" symbol="H"/>
+      <umod:element number="6" symbol="C"/>
+      <umod:element number="3" symbol="N"/>
+      <umod:element number="1" symbol="O"/>
+    </umod:aa>
+    <umod:aa avge_mass="113.1576" full_name="Isoleucine" mono_mass="113.084064" three_letter="Ile" title="I">
+      <umod:element number="11" symbol="H"/>
+      <umod:element number="6" symbol="C"/>
+      <umod:element number="1" symbol="N"/>
+      <umod:element number="1" symbol="O"/>
+    </umod:aa>
+    <umod:aa avge_mass="113.1576" full_name="Leucine" mono_mass="113.084064" three_letter="Leu" title="L">
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+      <umod:element number="6" symbol="C"/>
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+      <umod:element number="1" symbol="O"/>
+    </umod:aa>
+    <umod:aa avge_mass="128.1723" full_name="Lysine" mono_mass="128.094963" three_letter="Lys" title="K">
+      <umod:element number="12" symbol="H"/>
+      <umod:element number="6" symbol="C"/>
+      <umod:element number="2" symbol="N"/>
+      <umod:element number="1" symbol="O"/>
+    </umod:aa>
+    <umod:aa avge_mass="131.1961" full_name="Methionine" mono_mass="131.040485" three_letter="Met" title="M">
+      <umod:element number="9" symbol="H"/>
+      <umod:element number="5" symbol="C"/>
+      <umod:element number="1" symbol="N"/>
+      <umod:element number="1" symbol="O"/>
+      <umod:element number="1" symbol="S"/>
+    </umod:aa>
+    <umod:aa avge_mass="147.1739" full_name="Phenylalanine" mono_mass="147.068414" three_letter="Phe" title="F">
+      <umod:element number="9" symbol="H"/>
+      <umod:element number="9" symbol="C"/>
+      <umod:element number="1" symbol="N"/>
+      <umod:element number="1" symbol="O"/>
+    </umod:aa>
+    <umod:aa avge_mass="97.1152" full_name="Proline" mono_mass="97.052764" three_letter="Pro" title="P">
+      <umod:element number="7" symbol="H"/>
+      <umod:element number="5" symbol="C"/>
+      <umod:element number="1" symbol="N"/>
+      <umod:element number="1" symbol="O"/>
+    </umod:aa>
+    <umod:aa avge_mass="87.0773" full_name="Serine" mono_mass="87.032028" three_letter="Ser" title="S">
+      <umod:element number="5" symbol="H"/>
+      <umod:element number="3" symbol="C"/>
+      <umod:element number="1" symbol="N"/>
+      <umod:element number="2" symbol="O"/>
+    </umod:aa>
+    <umod:aa avge_mass="101.1039" full_name="Threonine" mono_mass="101.047679" three_letter="Thr" title="T">
+      <umod:element number="7" symbol="H"/>
+      <umod:element number="4" symbol="C"/>
+      <umod:element number="1" symbol="N"/>
+      <umod:element number="2" symbol="O"/>
+    </umod:aa>
+    <umod:aa avge_mass="186.2099" full_name="Tryptophan" mono_mass="186.079313" three_letter="Trp" title="W">
+      <umod:element number="10" symbol="H"/>
+      <umod:element number="11" symbol="C"/>
+      <umod:element number="2" symbol="N"/>
+      <umod:element number="1" symbol="O"/>
+    </umod:aa>
+    <umod:aa avge_mass="163.1733" full_name="Tyrosine" mono_mass="163.063329" three_letter="Tyr" title="Y">
+      <umod:element number="9" symbol="H"/>
+      <umod:element number="9" symbol="C"/>
+      <umod:element number="1" symbol="N"/>
+      <umod:element number="2" symbol="O"/>
+    </umod:aa>
+    <umod:aa avge_mass="99.1311" full_name="Valine" mono_mass="99.068414" three_letter="Val" title="V">
+      <umod:element number="9" symbol="H"/>
+      <umod:element number="5" symbol="C"/>
+      <umod:element number="1" symbol="N"/>
+      <umod:element number="1" symbol="O"/>
+    </umod:aa>
+    <umod:aa avge_mass="1.0079" full_name="N-term" mono_mass="1.007825" three_letter="N-term" title="N-term">
+      <umod:element number="1" symbol="H"/>
+    </umod:aa>
+    <umod:aa avge_mass="17.0073" full_name="C-term" mono_mass="17.002740" three_letter="C-term" title="C-term">
+      <umod:element number="1" symbol="H"/>
+      <umod:element number="1" symbol="O"/>
+    </umod:aa>
+  </umod:amino_acids>
+</umod:unimod>
+--gc0p4Jq0M2Yt08jU534c0p
+Content-Type: application/x-Mascot; name="enzyme"
+Title:Trypsin
+Cleavage:KR
+Restrict:P
+Cterm
+*
+--gc0p4Jq0M2Yt08jU534c0p
+Content-Type: application/x-Mascot; name="header"
+sequences=34724
+sequences_after_tax=34724
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+exec_time=2
+date=1364334220
+time=15:43:40
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+release=GbetaCCT_drome.fasta
+--gc0p4Jq0M2Yt08jU534c0p
+Content-Type: application/x-Mascot; name="summary"
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+h42=Q8T0E7,2.27e+01,1.00,71650.29
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+h44=Q9W4S7,2.23e+01,1.00,79714.56
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+h45=Q9W1V6,2.22e+01,1.00,79719.85
+h45_text=Diphenoloxidase subunit A3 OS=Drosophila melanogaster GN=Dox-A3 PE=1 SV=1
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+h46=Q4V4Y3,2.20e+01,1.00,76639.93
+h46_text=IP12842p (Fragment) OS=Drosophila melanogaster GN=CG13283 PE=2 SV=1
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+h47=Q3YNF4,2.18e+01,0.50,2377.20
+h47_text=CG6547 (Fragment) OS=Drosophila melanogaster GN=mRpL37 PE=2 SV=1
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+h47_q1_terms=-,K
+h47_q2=-1
+h48=Q9VJH0,2.18e+01,1.00,78413.94
+h48_text=CG13283 OS=Drosophila melanogaster GN=CG13283 PE=2 SV=1
+h48_q1=1,2113.077850,-0.077754,137,153,0.00,LTSHWERMLDEIPFLAR,0,0000000000000000000,0.00,1,0000000000000000000,0,0,0.000000
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+h49=A8JNT5,2.15e+01,1.00,87547.51
+h49_text=Myosin binding subunit, isoform G OS=Drosophila melanogaster GN=Mbs PE=4 SV=1
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+h50=Q9VB58,2.14e+01,1.00,84861.77
+h50_text=AT11276p OS=Drosophila melanogaster GN=CG5987 PE=2 SV=1
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+q2_p6=0,2978.688492,0.776544,8,GAEFSSFSVVLLVIILIIVFLSNAYHK,118,00000000000000000000000000000,1.07,0000020000000000000,0,0;"A8DYF1":0:2:28:1
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+Content-Type: application/x-Mascot; name="proteins"
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+--gc0p4Jq0M2Yt08jU534c0p
+Content-Type: application/x-Mascot; name="query1"
+title=1%2e2746%2e2746%2e2
+index=1
+charge=2+
+mass_min=305.484440
+mass_max=1998.945430
+int_min=1.5
+int_max=747
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+--gc0p4Jq0M2Yt08jU534c0p
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+--gc0p4Jq0M2Yt08jU534c0p
+Content-Type: application/x-Mascot; name="index"
+parameters=4
+masses=78
+unimod=119
+enzyme=484
+header=492
+summary=507
+peptides=820
+proteins=853
+query1=858
+query2=871
+--gc0p4Jq0M2Yt08jU534c0p--