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comparison test-data/201208-378803-mm.pepXML @ 2:dd33125925d9 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 1e51bed3a1c10c67ef0404216608e9333db04c64
author galaxyp
date Fri, 06 Oct 2017 15:00:48 -0400
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1:ee69ea5752fe 2:dd33125925d9
1 <?xml version="1.0" encoding="ISO-8859-1"?>
2 <msms_pipeline_analysis date="2015-09-03T15:49:50" summary_xml="201208-378803.pepXML" xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v117.xsd">
3 <analysis_summary analysis="MyriMatch" version="2.2.8634" time="2015-09-03T15:49:50"/>
4 <msms_run_summary base_name="201208-378803" raw_data_type="" raw_data="">
5 <sample_enzyme name="Trypsin/P" independent="false" fidelity="semispecific">
6 <specificity sense="C" cut="KR" no_cut="" min_spacing="1"/>
7 </sample_enzyme>
8 <search_summary base_name="201208-378803" search_engine="MyriMatch" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" out_data_type="" out_data="">
9 <search_database local_path="cow.protein.PRG2012-subset.fasta" database_name="SDB" type="AA"/>
10 <enzymatic_search_constraint enzyme="Trypsin/P" max_num_internal_cleavages="2" min_number_termini="1"/>
11 <aminoacid_modification aminoacid="M" massdiff="15.9949" mass="147.0353846062" variable="Y" description="Oxidation"/>
12 <aminoacid_modification aminoacid="Q" massdiff="-17.026" mass="111.0325775114" peptide_terminus="n" variable="Y"/>
13 <aminoacid_modification aminoacid="Q" massdiff="0.984016" mass="129.0425935114" variable="Y" description="Deamidated"/>
14 <aminoacid_modification aminoacid="N" massdiff="0.984016" mass="115.0269434472" variable="Y" description="Deamidated"/>
15 <aminoacid_modification aminoacid="C" massdiff="58.00548" mass="161.0146644778" variable="N" description="Carboxymethyl"/>
16 <parameter name="Config: AvgPrecursorMzTolerance" value="1.5mz"/>
17 <parameter name="Config: ClassSizeMultiplier" value="2"/>
18 <parameter name="Config: CleavageRules" value="Trypsin/P"/>
19 <parameter name="Config: ComputeXCorr" value="1"/>
20 <parameter name="Config: DecoyPrefix" value="XXX_"/>
21 <parameter name="Config: DynamicMods" value="M * 15.9949 (Q * -17.026 [QN] * 0.984016"/>
22 <parameter name="Config: EstimateSearchTimeOnly" value="0"/>
23 <parameter name="Config: FragmentMzTolerance" value="0.5mz"/>
24 <parameter name="Config: FragmentationAutoRule" value="1"/>
25 <parameter name="Config: FragmentationRule" value="cid"/>
26 <parameter name="Config: KeepUnadjustedPrecursorMz" value="0"/>
27 <parameter name="Config: MaxDynamicMods" value="2"/>
28 <parameter name="Config: MaxFragmentChargeState" value="0"/>
29 <parameter name="Config: MaxMissedCleavages" value="2"/>
30 <parameter name="Config: MaxPeakCount" value="300"/>
31 <parameter name="Config: MaxPeptideLength" value="75"/>
32 <parameter name="Config: MaxPeptideMass" value="10000"/>
33 <parameter name="Config: MaxPeptideVariants" value="1000000"/>
34 <parameter name="Config: MaxResultRank" value="3"/>
35 <parameter name="Config: MinMatchedFragments" value="5"/>
36 <parameter name="Config: MinPeptideLength" value="5"/>
37 <parameter name="Config: MinPeptideMass" value="0"/>
38 <parameter name="Config: MinResultScore" value="9.9999999999999995e-08"/>
39 <parameter name="Config: MinTerminiCleavages" value="1"/>
40 <parameter name="Config: MonoPrecursorMzTolerance" value="50ppm"/>
41 <parameter name="Config: MonoisotopeAdjustmentSet" value="[-1,2] "/>
42 <parameter name="Config: NumBatches" value="50"/>
43 <parameter name="Config: NumChargeStates" value="5"/>
44 <parameter name="Config: NumIntensityClasses" value="3"/>
45 <parameter name="Config: NumMzFidelityClasses" value="3"/>
46 <parameter name="Config: OutputFormat" value="pepXML"/>
47 <parameter name="Config: OutputSuffix" value=""/>
48 <parameter name="Config: PrecursorMzToleranceRule" value="mono"/>
49 <parameter name="Config: PreferIntenseComplements" value="1"/>
50 <parameter name="Config: ProteinDatabase" value="cow.protein.PRG2012-subset.fasta"/>
51 <parameter name="Config: ProteinListFilters" value=""/>
52 <parameter name="Config: ProteinSamplingTime" value="15"/>
53 <parameter name="Config: ResultsPerBatch" value="200000"/>
54 <parameter name="Config: SpectrumListFilters" value="peakPicking true 2-"/>
55 <parameter name="Config: StaticMods" value="C 58.00548"/>
56 <parameter name="Config: StatusUpdateFrequency" value="5"/>
57 <parameter name="Config: TicCutoffPercentage" value="0.97999999999999998"/>
58 <parameter name="Config: UseMultipleProcessors" value="1"/>
59 <parameter name="Config: UseSmartPlusThreeModel" value="0"/>
60 <parameter name="Config: WorkingDirectory" value="/galaxy-central"/>
61 <parameter name="PeakCounts: 1stQuartile: Filtered" value="115"/>
62 <parameter name="PeakCounts: 1stQuartile: Original" value="120"/>
63 <parameter name="PeakCounts: 2ndQuartile: Filtered" value="145"/>
64 <parameter name="PeakCounts: 2ndQuartile: Original" value="154"/>
65 <parameter name="PeakCounts: 3rdQuartile: Filtered" value="177"/>
66 <parameter name="PeakCounts: 3rdQuartile: Original" value="180"/>
67 <parameter name="PeakCounts: Mean: Filtered" value="149"/>
68 <parameter name="PeakCounts: Mean: Original" value="157"/>
69 <parameter name="PeakCounts: Min/Max: Filtered" value="40 / 296"/>
70 <parameter name="PeakCounts: Min/Max: Original" value="42 / 471"/>
71 <parameter name="SearchEngine: Name" value="MyriMatch"/>
72 <parameter name="SearchEngine: Version" value="2.2.8634"/>
73 <parameter name="SearchStats: Nodes" value="1"/>
74 <parameter name="SearchStats: Overall" value="144 proteins; 516261 peptides; 2500621 variants; 1034167 comparisons"/>
75 <parameter name="SearchTime: Duration" value="15.5659609 seconds"/>
76 <parameter name="SearchTime: Started" value="15:49:34 on 09/03/2015"/>
77 <parameter name="SearchTime: Stopped" value="15:49:50 on 09/03/2015"/>
78 </search_summary>
79 <spectrum_query spectrum="201208-378803.1.1.2" spectrumNativeID="sample=1 period=1 cycle=1181 experiment=2" start_scan="1" end_scan="1" precursor_neutral_mass="1011.474906260116" assumed_charge="2" index="1" retention_time_sec="614.35099999998">
80 <search_result num_target_comparisons="0" num_decoy_comparisons="0">
81 <search_hit hit_rank="1" peptide="RSPALGAANR" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|27806851|ref|NP_776358.1|" num_tot_proteins="4" calc_neutral_pep_mass="1011.557375519" massdiff="0.082469258884" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="9" tot_num_ions="19">
82 <alternative_protein protein="gi|528993971|ref|XP_005219929.1|"/>
83 <alternative_protein protein="gi|528993973|ref|XP_005219930.1|"/>
84 <alternative_protein protein="gi|528993975|ref|XP_005219931.1|"/>
85 <search_score name="mvh" value="20.943884244483"/>
86 <search_score name="mzFidelity" value="40.011435006046"/>
87 <search_score name="xcorr" value="2.113353934546164"/>
88 </search_hit>
89 <search_hit hit_rank="2" peptide="RSPALGAANR" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|27806851|ref|NP_776358.1|" num_tot_proteins="4" calc_neutral_pep_mass="1012.541391519" massdiff="0.057820343284" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="8" tot_num_ions="19">
90 <alternative_protein protein="gi|528993971|ref|XP_005219929.1|"/>
91 <alternative_protein protein="gi|528993973|ref|XP_005219930.1|"/>
92 <alternative_protein protein="gi|528993975|ref|XP_005219931.1|"/>
93 <modification_info>
94 <mod_aminoacid_mass position="9" mass="115.0269434472"/>
95 </modification_info>
96 <search_score name="mvh" value="19.008347302137"/>
97 <search_score name="mzFidelity" value="35.588423710657"/>
98 <search_score name="xcorr" value="1.9616309176657931"/>
99 </search_hit>
100 <search_hit hit_rank="3" peptide="QLPKSNAPR" peptide_prev_aa="K" peptide_next_aa="V" protein="gi|32880221|ref|NP_872593.1|" num_tot_proteins="1" calc_neutral_pep_mass="1010.5508935728" massdiff="0.084652228284" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="6" tot_num_ions="17">
101 <modification_info>
102 <mod_aminoacid_mass position="6" mass="115.0269434472"/>
103 </modification_info>
104 <search_score name="mvh" value="12.941640349312"/>
105 <search_score name="mzFidelity" value="27.424896373573"/>
106 <search_score name="xcorr" value="1.3971794629675336"/>
107 </search_hit>
108 <search_hit hit_rank="4" peptide="EDPQDAIPK" peptide_prev_aa="L" peptide_next_aa="G" protein="gi|297479727|ref|XP_002690982.1|" num_tot_proteins="2" calc_neutral_pep_mass="1012.4713058478" massdiff="-0.012265327916" num_tol_term="1" num_missed_cleavages="0" num_matched_ions="5" tot_num_ions="17">
109 <alternative_protein protein="gi|528966552|ref|XP_005211956.1|"/>
110 <modification_info>
111 <mod_aminoacid_mass position="4" mass="129.0425935114"/>
112 </modification_info>
113 <search_score name="mvh" value="10.776069653902"/>
114 <search_score name="mzFidelity" value="21.773698015738"/>
115 <search_score name="xcorr" value="0.714776080009772"/>
116 </search_hit>
117 <search_hit hit_rank="5" peptide="NAAGLAPSRR" peptide_prev_aa="R" peptide_next_aa="N" protein="XXX_gi|27806851|ref|NP_776358.1|" num_tot_proteins="3" calc_neutral_pep_mass="1011.557375519" massdiff="0.082469258884" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="5" tot_num_ions="19">
118 <alternative_protein protein="XXX_gi|528993971|ref|XP_005219929.1|"/>
119 <alternative_protein protein="XXX_gi|528993973|ref|XP_005219930.1|"/>
120 <search_score name="mvh" value="10.229701455942"/>
121 <search_score name="mzFidelity" value="22.932400378615"/>
122 <search_score name="xcorr" value="0.90139108915810939"/>
123 </search_hit>
124 <search_hit hit_rank="6" peptide="DQDILNHR" peptide_prev_aa="M" peptide_next_aa="V" protein="XXX_gi|528944676|ref|XP_005204734.1|" num_tot_proteins="1" calc_neutral_pep_mass="1010.4781225602" massdiff="0.011881215684" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="5" tot_num_ions="15">
125 <modification_info>
126 <mod_aminoacid_mass position="6" mass="115.0269434472"/>
127 </modification_info>
128 <search_score name="mvh" value="10.003747281739"/>
129 <search_score name="mzFidelity" value="25.386798535619"/>
130 <search_score name="xcorr" value="1.2327418458265254"/>
131 </search_hit>
132 </search_result>
133 </spectrum_query>
134 <spectrum_query spectrum="201208-378803.1.1.4" spectrumNativeID="sample=1 period=1 cycle=1181 experiment=2" start_scan="1" end_scan="1" precursor_neutral_mass="2022.949812520232" assumed_charge="4" index="2" retention_time_sec="614.35099999998">
135 <search_result num_target_comparisons="0" num_decoy_comparisons="0">
136 <search_hit hit_rank="1" peptide="VRAAALKLGQELCGMLHR" peptide_prev_aa="L" peptide_next_aa="P" protein="gi|528921178|ref|XP_592304.7|" num_tot_proteins="3" calc_neutral_pep_mass="2023.0819199626" massdiff="0.132107442368" num_tol_term="1" num_missed_cleavages="2" num_matched_ions="19" tot_num_ions="99">
137 <alternative_protein protein="gi|528921180|ref|XP_005195747.1|"/>
138 <alternative_protein protein="gi|528995523|ref|XP_002695913.2|"/>
139 <modification_info>
140 <mod_aminoacid_mass position="13" mass="161.0146644778"/>
141 </modification_info>
142 <search_score name="mvh" value="21.467037536913"/>
143 <search_score name="mzFidelity" value="19.37024464526"/>
144 <search_score name="xcorr" value="2.2623632236296167"/>
145 </search_hit>
146 <search_hit hit_rank="2" peptide="AQDTGLPFTGKERDPPVPP" peptide_prev_aa="R" peptide_next_aa="F" protein="XXX_gi|297488451|ref|XP_002696970.1|" num_tot_proteins="4" calc_neutral_pep_mass="2021.0218046597" massdiff="0.089321970668" num_tol_term="1" num_missed_cleavages="2" num_matched_ions="16" tot_num_ions="102">
147 <alternative_protein protein="XXX_gi|358418103|ref|XP_600387.4|"/>
148 <alternative_protein protein="XXX_gi|528923273|ref|XP_005196452.1|"/>
149 <alternative_protein protein="XXX_gi|529000951|ref|XP_005222651.1|"/>
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151 <search_score name="mzFidelity" value="20.708945557204"/>
152 <search_score name="xcorr" value="1.7484519315798444"/>
153 </search_hit>
154 <search_hit hit_rank="3" peptide="VRAAALKLGQELCGMLHR" peptide_prev_aa="L" peptide_next_aa="P" protein="gi|528921178|ref|XP_592304.7|" num_tot_proteins="3" calc_neutral_pep_mass="2024.0659359626" massdiff="0.107458526768" num_tol_term="1" num_missed_cleavages="2" num_matched_ions="18" tot_num_ions="99">
155 <alternative_protein protein="gi|528921180|ref|XP_005195747.1|"/>
156 <alternative_protein protein="gi|528995523|ref|XP_002695913.2|"/>
157 <modification_info>
158 <mod_aminoacid_mass position="10" mass="129.0425935114"/>
159 <mod_aminoacid_mass position="13" mass="161.0146644778"/>
160 </modification_info>
161 <search_score name="mvh" value="19.477768930341"/>
162 <search_score name="mzFidelity" value="19.862979428176"/>
163 <search_score name="xcorr" value="2.5029671826385758"/>
164 </search_hit>
165 <search_hit hit_rank="4" peptide="AAALKLGQELCGMLHRPR" peptide_prev_aa="R" peptide_next_aa="H" protein="gi|528995523|ref|XP_002695913.2|" num_tot_proteins="1" calc_neutral_pep_mass="2021.0662698984" massdiff="0.133787209368" num_tol_term="2" num_missed_cleavages="2" num_matched_ions="15" tot_num_ions="96">
166 <modification_info>
167 <mod_aminoacid_mass position="11" mass="161.0146644778"/>
168 </modification_info>
169 <search_score name="mvh" value="15.095047502377"/>
170 <search_score name="mzFidelity" value="16.115018508678"/>
171 <search_score name="xcorr" value="1.9267737457763163"/>
172 </search_hit>
173 <search_hit hit_rank="5" peptide="PRHLMGCLEQGLKLAAAR" peptide_prev_aa="R" peptide_next_aa="V" protein="XXX_gi|528995523|ref|XP_002695913.2|" num_tot_proteins="1" calc_neutral_pep_mass="2021.0662698984" massdiff="0.133787209368" num_tol_term="2" num_missed_cleavages="2" num_matched_ions="13" tot_num_ions="99">
174 <modification_info>
175 <mod_aminoacid_mass position="7" mass="161.0146644778"/>
176 </modification_info>
177 <search_score name="mvh" value="12.532513600259"/>
178 <search_score name="mzFidelity" value="12.691293478724"/>
179 <search_score name="xcorr" value="1.32307615270207"/>
180 </search_hit>
181 </search_result>
182 </spectrum_query>
183 <spectrum_query spectrum="201208-378803.1.1.5" spectrumNativeID="sample=1 period=1 cycle=1181 experiment=2" start_scan="1" end_scan="1" precursor_neutral_mass="2526.66993581909" assumed_charge="5" index="3" retention_time_sec="614.35099999998">
184 <search_result num_target_comparisons="0" num_decoy_comparisons="0">
185 <search_hit hit_rank="1" peptide="LELLLQIANKIQNGALNCEEKL" peptide_prev_aa="R" peptide_next_aa="T" protein="gi|219804516|ref|NP_001137332.1|" num_tot_proteins="3" calc_neutral_pep_mass="2526.3251069949" massdiff="-0.34482882419" num_tol_term="1" num_missed_cleavages="2" num_matched_ions="25" tot_num_ions="154">
186 <alternative_protein protein="gi|528944676|ref|XP_005204734.1|"/>
187 <alternative_protein protein="gi|528944678|ref|XP_005204735.1|"/>
188 <modification_info>
189 <mod_aminoacid_mass position="12" mass="129.0425935114"/>
190 <mod_aminoacid_mass position="17" mass="115.0269434472"/>
191 <mod_aminoacid_mass position="18" mass="161.0146644778"/>
192 </modification_info>
193 <search_score name="mvh" value="24.555168021719"/>
194 <search_score name="mzFidelity" value="13.158130753361"/>
195 <search_score name="xcorr" value="2.6769549653109732"/>
196 </search_hit>
197 <search_hit hit_rank="1" peptide="LELLLQIANKIQNGALNCEEKL" peptide_prev_aa="R" peptide_next_aa="T" protein="gi|219804516|ref|NP_001137332.1|" num_tot_proteins="3" calc_neutral_pep_mass="2526.3251069949" massdiff="-0.34482882419" num_tol_term="1" num_missed_cleavages="2" num_matched_ions="25" tot_num_ions="154">
198 <alternative_protein protein="gi|528944676|ref|XP_005204734.1|"/>
199 <alternative_protein protein="gi|528944678|ref|XP_005204735.1|"/>
200 <modification_info>
201 <mod_aminoacid_mass position="13" mass="115.0269434472"/>
202 <mod_aminoacid_mass position="17" mass="115.0269434472"/>
203 <mod_aminoacid_mass position="18" mass="161.0146644778"/>
204 </modification_info>
205 <search_score name="mvh" value="24.555168021719"/>
206 <search_score name="mzFidelity" value="13.158130753361"/>
207 <search_score name="xcorr" value="2.6858516440138747"/>
208 </search_hit>
209 <search_hit hit_rank="2" peptide="QERLALEATIKDNESEEGNGGIR" peptide_prev_aa="E" peptide_next_aa="G" protein="gi|297479727|ref|XP_002690982.1|" num_tot_proteins="4" calc_neutral_pep_mass="2530.214704231" massdiff="0.518773665111" num_tol_term="1" num_missed_cleavages="2" num_matched_ions="25" tot_num_ions="162">
210 <alternative_protein protein="gi|358414198|ref|XP_002700672.2|"/>
211 <alternative_protein protein="gi|528966552|ref|XP_005211956.1|"/>
212 <alternative_protein protein="gi|528966554|ref|XP_005211957.1|"/>
213 <modification_info>
214 <mod_aminoacid_mass position="13" mass="115.0269434472"/>
215 <mod_aminoacid_mass position="19" mass="115.0269434472"/>
216 </modification_info>
217 <search_score name="mvh" value="22.75395632061"/>
218 <search_score name="mzFidelity" value="24.10812825654"/>
219 <search_score name="xcorr" value="3.2616588403384505"/>
220 </search_hit>
221 <search_hit hit_rank="3" peptide="LELLLQIANKIQNGALNCEEKL" peptide_prev_aa="R" peptide_next_aa="T" protein="gi|219804516|ref|NP_001137332.1|" num_tot_proteins="3" calc_neutral_pep_mass="2526.3251069949" massdiff="-0.34482882419" num_tol_term="1" num_missed_cleavages="2" num_matched_ions="24" tot_num_ions="154">
222 <alternative_protein protein="gi|528944676|ref|XP_005204734.1|"/>
223 <alternative_protein protein="gi|528944678|ref|XP_005204735.1|"/>
224 <modification_info>
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228 </modification_info>
229 <search_score name="mvh" value="22.352043722256"/>
230 <search_score name="mzFidelity" value="10.775997964917"/>
231 <search_score name="xcorr" value="2.5918696638942031"/>
232 </search_hit>
233 <search_hit hit_rank="4" peptide="GVTVAQHVDAAHSEIEEELAKHR" peptide_prev_aa="Q" peptide_next_aa="I" protein="XXX_gi|528944678|ref|XP_005204735.1|" num_tot_proteins="1" calc_neutral_pep_mass="2526.2462787157" massdiff="-0.42365710339" num_tol_term="1" num_missed_cleavages="1" num_matched_ions="22" tot_num_ions="159">
234 <modification_info>
235 <mod_aminoacid_mass position="6" mass="129.0425935114"/>
236 </modification_info>
237 <search_score name="mvh" value="19.580449224809"/>
238 <search_score name="mzFidelity" value="13.402506848624"/>
239 <search_score name="xcorr" value="2.9697220446115864"/>
240 </search_hit>
241 <search_hit hit_rank="5" peptide="QMLDLLDIKEATNPDILNKSSR" peptide_prev_aa="R" peptide_next_aa="L" protein="XXX_gi|528944676|ref|XP_005204734.1|" num_tot_proteins="1" calc_neutral_pep_mass="2530.2948537701" massdiff="0.59892320421" num_tol_term="2" num_missed_cleavages="2" num_matched_ions="16" tot_num_ions="155">
242 <modification_info>
243 <mod_aminoacid_mass position="2" mass="147.0353846062"/>
244 <mod_aminoacid_mass position="18" mass="115.0269434472"/>
245 </modification_info>
246 <search_score name="mvh" value="15.920923377675"/>
247 <search_score name="mzFidelity" value="11.187293576294"/>
248 <search_score name="xcorr" value="1.3435728884597988"/>
249 </search_hit>
250 <search_hit hit_rank="6" peptide="THFQHLLKSMENEDKEETVAK" peptide_prev_aa="K" peptide_next_aa="M" protein="gi|528944678|ref|XP_005204735.1|" num_tot_proteins="1" calc_neutral_pep_mass="2530.2009533849" massdiff="0.50502281901" num_tol_term="2" num_missed_cleavages="2" num_matched_ions="17" tot_num_ions="145">
251 <modification_info>
252 <mod_aminoacid_mass position="10" mass="147.0353846062"/>
253 <mod_aminoacid_mass position="12" mass="115.0269434472"/>
254 </modification_info>
255 <search_score name="mvh" value="14.521473880124"/>
256 <search_score name="mzFidelity" value="10.1620270721"/>
257 <search_score name="xcorr" value="1.5544656865133089"/>
258 </search_hit>
259 </search_result>
260 </spectrum_query>
261 <spectrum_query spectrum="201208-378803.2.2.2" spectrumNativeID="sample=1 period=1 cycle=1183 experiment=2" start_scan="2" end_scan="2" precursor_neutral_mass="830.315296606328" assumed_charge="2" index="4" retention_time_sec="617.50600000002">
262 <search_result num_target_comparisons="3908" num_decoy_comparisons="4324">
263 <search_hit hit_rank="1" peptide="EDVPSER" peptide_prev_aa="K" peptide_next_aa="Y" protein="gi|30794348|ref|NP_851372.1|" num_tot_proteins="6" calc_neutral_pep_mass="830.3770111169" massdiff="0.061714510572" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="8" tot_num_ions="13">
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