Repository 'mz_to_sqlite'
hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/mz_to_sqlite

Changeset 2:1320693cbf1e (2019-02-11)
Previous changeset 1:e34bdac5b157 (2018-03-28) Next changeset 3:728d459bafe8 (2020-06-29)
Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit ae0093d9f1576f38aee83b2ed5e7f70c901d5864
modified:
mz_to_sqlite.xml
added:
test-data/sqlite.db
test-data/test.fasta
test-data/test.mgf
test-data/test_id.mzid
b
diff -r e34bdac5b157 -r 1320693cbf1e mz_to_sqlite.xml
--- a/mz_to_sqlite.xml Wed Mar 28 09:33:18 2018 -0400
+++ b/mz_to_sqlite.xml Mon Feb 11 17:30:46 2019 -0500
b
@@ -1,7 +1,7 @@
-<tool id="mz_to_sqlite" name="mz to sqlite" version="2.0.0">
+<tool id="mz_to_sqlite" name="mz to sqlite" version="2.0.2">
     <description>Extract mzIdentML and associated proteomics datasets into a SQLite DB</description>
     <requirements>
-      <requirement type="package" version="2.0.0">mztosqlite</requirement>
+      <requirement type="package" version="2.0.2">mztosqlite</requirement>
     </requirements>
    <stdio>
        <exit_code range="1:"  level="fatal" description="Error Running mz_to_sqlite" />
@@ -38,6 +38,10 @@
     </outputs>
     <tests>
         <test>
+            <param name="mzinput" value="test_id.mzid" ftype="mzid"></param>
+            <param name="scanfiles" value="test.mgf" ftype="mgf"></param>
+            <param name="searchdbs" value="test.fasta" ftype="fasta"></param>
+            <output name="sqlite_db" file="sqlite.db" />
         </test>
     </tests>
     <help>
@@ -46,4 +50,5 @@
 
 ]]>
     </help>
+    <citations></citations>
 </tool>
b
diff -r e34bdac5b157 -r 1320693cbf1e test-data/sqlite.db
b
Binary file test-data/sqlite.db has changed
b
diff -r e34bdac5b157 -r 1320693cbf1e test-data/test.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.fasta Mon Feb 11 17:30:46 2019 -0500
b
b'@@ -0,0 +1,26 @@\n+>sp|Q8C4J7|TBL3_MOUSE Transducin beta-like protein 3 OS=Mus musculus GN=Tbl3 PE=2 SV=1\n+MAETAAGLCRFKANYAVERKIEPFYKGGKAQLDQTGHYLFCVCGTKVNILDVASGALLRSLEQEDQEDITSFDLSPDDEVLVTASRALLLAQWAWREGTVTRLWKAIHTAPVASMAFDATSTLLATGGCDGAVRVWDIVQHYGTHHFRGSPGVVHLVAFHPDPTRLLLFSSAVDTSIRVWSLQDRSCLAVLTAHYSAVTSLSFSEGGHTMLSSGRDKICIVWDLQSYQTTRTVPVFESVEASVLLPEQPAPALGVKSSGLHFLTAGDQGILRVWEAASGQCVYTQPQMPGLRQELTHCTLARAADLLLTVTADHNLLLYEAHSLQLQKQFAGYSEEVLDVRFLGPSDSHIVVASNSPCLKVFELQTLACQILHGHTDIVLALDVFRKGWLFASCAKDQSIRIWKMNKAGQVACVAQGSGHTHSVGTICCSRLKESFLVTGSQDCTVKLWPLPEALLAKSTAADSGPVLLQAQTTRRCHDKDINSLAVSPNDKLLATGSQDRTAKLWALPQCQLLGVFTGHRRGLWNVQFSPTDQVLATASADGTIKLWALQDFSCLKTFEGHDASVLKVAFVSRGSQLLSSGSDGLLKLWTIKSNECVRTLDAHEDKVWGLHCSQLDDHAITGGSDSRIILWKDVTEAEQAEEQAKREEQVIKQQELDNLLHEKRYLRALGLAISLDRPHTVLTVIQAIRRDPEACEKLEATVLRLRRDQKEALLRFCVTWNTNSRHCHEAQAVLGVLLRHEAPEELLAYDGVRGSLEALLPYTERHFQRLSRTLQAATFLDFLWHNMKLSPCPAAAPPAL\n+>tr|Q80ZP8|Q80ZP8_MOUSE Armet protein OS=Mus musculus GN=Manf PE=1 SV=1\n+METNNYLPSPPSFPVCISYLGRFYQDLKDRDVTFSPATIEEELIKFCREARGKENRLCYYIGATDDAATKIINEVSKPLAHHIPVEKICEKLKKKDSQICELKYDKQIDLSTVDLKKLRVKELKKILDDWGEMCKGCAEKSDYIRKINELMPKYAPKAASARTDL\n+>sp|Q60847|COCA1_MOUSE Collagen alpha-1(XII) chain OS=Mus musculus GN=Col12a1 PE=2 SV=3\n+MQTRLPRALAALGVALLLSSIEAEVDPPSDLNFKIIDENTVHMSWERPVDPIVGYRITVDPTTDGPTKEFTLAASTTETLLSDLIPETQYVVTITSYNEVEESVPVIGQLTIQTGGPTKPGEKKPGKTEIQKCSVSAWTDLVFLVDGSWSVGRNNFKYILDFIVALVSAFDIGEEKTRVGVVQYSSDTRTEFNLNQYYRREDLLAAVKKIPYKGGNTMTGDAIDYLVKNTFTESAGSRAGFPKVAIIITDGKSQDEVEIPARELRNIGVEVFSLGIKAADAKELKQIASTPSLNHVFNVANFDAIVDIQNEIISQVCSGVDEQLGELVSGEEVIEPPSNLVVTELSSKYIRLSWDPSPSAVTGYKILLTPMAAGSRHHALSVGPQTTTLNVRDLTADTEYQISVFAMKGLTSSEPTSVMEKTQPMKVQVECSRGVDIKADIVFLVDGSYSIGIANFVKVRAFLEVLAKSFEISPNRVQISLVQYSRDPHTEFTLKEFNRVEDIIKAINTFPYRGGSTNTGKAMTYVREKIFVPNKGSRSNVPKVMILITDGKSSDAFRDPAIKLRNSDVEIFAVGVKDAVRSELEAIASPPAETHVFTVEDFDAFQRISFELTQSICLRIEQELAAIKKKAYVPPKDLRFTQVTANSFKAEWSPPGDNVFSYHVTYKDANGDDEVTVVEPASSTSVVLNNLRPETLYLVNVTAEYEDGFSVPITGEETTAEVKGVPRNLKVTDETTDSFKLTWSQAPGRVLRYRIRYRPVSGGESKEVSTPANQRRKTLENLTPDTKYEISVIAEYSSGPGSPLTGNAATEEVRGNPRDLRVSDATTSTLKLSWSRAPGKVKQYLVTYTPAAGGETQEVTVRGDTTTTMLRKLKEGTQYDLSVTALYASGAGEALSGKGSTLEERGSPQNLVTKDITDTSIGAYWTSAPGMVRGYRVSWKSLYDDIEAGETTLPGDAIHTMIENLQPETKYKISVFATYSSGEGEPVTGDATTELSQDSKILRVDEETEHTMRVTWKAAPGKVVNYRVVYRPQGGGRQMVAKVPPTVTSTVLKRLQPQTTYDITVLPMYKTGEGKLRQGSGTTASRFKSPRNLKTSDPTMSSFRVTWEPAPGEVKGYKVTFHPTGDDRRLGELVLGPYDNTVVLEELRAGTTYRVNVFGMFDGGESLPLVGQEMTTLSDTTVTPFLSSGMDCLTRAEADIVLLVDGSWSIGRANFRTVRSFISRIVEVFEIGPKRVQIALAQYSGDPRTEWQLNAHRDKKSLLQAVANLPYKGGNTLTGMALNFIRQQSFKTQAGMRPRARKIGVLITDGKSQDDVEAPSKKLKDEGVELFAIGIKNADEVELKMIATDPDDTHAYNVADFESLSKIVDDLTINLCNSVKGPGDLEAPTNLVISERTHRSFRVSWTPPSDSVDRYKVEYYPVSGGKRQEFYVSRLDTSTVLKDLKPETDYVVNVYSVVEDEYSEPLKGTEKTLPVPVVSLNIYDVGPTTMHVQWQPVGGATGYTVSYQPTRSPEGTKPKEMRVGPTVNDVQLTGLLPNTEYEVTVQAVLYDLTSEPAKAREVTLPLPRPQDVKLRDVTHSTMNVVWEPVLGKVRKYIVRYKTPDEEFKEVEVDRSRASTILKDLSSQTQYTVSVSAVYDEGTSPPATAYDTTRRVPAPTNLQFTEVTPESFRGTWDHGASDVSLYRITWAPVGNPDKMETILNGDENTLVFENLNPNTPYEVSITAIYPDESESEDLSGTERTLRLIPLTTQAPKSGPRNLQVYNATSNSLTVKWDPASGRVQKYRITYQPSTGEGNEQTITVGGRQNSVLLQKLKPDTPYTITVYSQYPDGEGGRMTGRGKTKPLNTVRNLRVYDPSTSSLSVRWDHAEGNPRQYKLFYAPTSGGPEELVPIPGNTNYAILRNLQPDTPYTITVVPVYTEGDGGRTSDTGRTLVRGLARNIQVYNPTPNSLDVRWDPAPGPVQQYRIVYSPVAGTRPSESIVVPGNTRTVHLERLIPDTPYSVNIVALYSDGEGNPSPSQGRTLPRSGPRNIRVFGETTNSLSVAWDHADGPVQQYRIIYSPTVGDPIDEYTTVPGRRNNVILQPLQPDTPYKITVIAIYEDGDGGHLTGNGRTVGLLPPQNIHIFDEWYTRFRVSWDPSPSPVLGYKIVYKPVGSNEPMEAFVGEVTSYTLHNLNPSTTYDVSVYAQYDSGLSVPLTDQGTTLYLNVTDLKTYQVGWDTFCVKWSPHRAATSYRLKLSPADGTRGQEITVRGSETSHCFTGLSPEAEYGVTVFVQTPNLEGPGVPIKEQTTVKPTEAPTEPPTPSPPPTIPPARDVCKGAKADIVFLTDASWSIGDDNFNKVVKFIFNTVGAFDEVNPAGIQVSFVQYSDEVKSEFKLNTYNDKALALGALQNIRYRGGNTRTGKALTFIKEKVLTWESGMRKNVPKVLVVVTDGRSQDEVKKAAFVIQQSGFSVFVVGVADVDYNELANIASKPSERHVFIVDDFESFEKIEDNLITFVCETATSSCPLIYLDGYTSPGFKMLEAYNLTEKNFASVQGVSLESGSFPSYSAYRLQKNAFINQPTAELHPNGLPPSYTIILLFRLLPETPSDPFAIWQITDRDYRPQVGVIADPSSKTLSFFNKDTRGEVQTVTFDTDEVKTLFYGSFHKVHIVVTSKSVKIYIDCYEIIEKDIKEAGNITTDGYEILGKLLKGERKSATFQIQSFDIVCSPVWTSRDRCCDIPSRRDEAKCPALPNACTCTQDSVGPPGPPGPAGGPG'..b'RAGFRSNVLTGSAPQQDFDKLKALGGENSSKTGVSTSGHTDKNKVKREAESNSITLSVYEPFKVRKAEDKLKENSEKMLESRVLDGKPSSEKSDSGIAAAASSKTKPSSKLSSCIAAIAALSAKKAASDSCKEPVANSREASPLPKEVNDSPKAADKSPESQNLIDGTKKASLKPSDSPRSVSSENSSKGSPSSPVGSTPAIPKVRIKTIKTSSGEIKRTVTRVLPEVDLDSGKKPSEQAASVMASVTSLLSSSASATVLSSPPRAPLQTAMVTSAVSSAELTPKQVTIKPVATAFLPVSAVKTAGSQVINLKLANNTTVKATVISAASVQSASSAIIKAANAIQQQTVVVPASSLANAKLVPKTVHLANLNLLPQGAQATSELRQVLTKPQQQIKQAIINAAASQPPKKVSRVQVVSSLQSSVVEAFNKVLSSVNPVPVYTPNLSPPANAGITLPMRGYKCLECGDAFALEKSLSQHYDRRSVRIEVTCNHCTKNLVFYNKCSLLSHARGHKEKGVVMQCSHLILKPVPADQMIVPPSSNTAASTLQSSVGAATHTVPKVQPGIAGAVISAPASTPMSPAMPLDEDPSKLCRHSLKCLECNEVFQDEPSLATHFQHAADTSGQQMKKHPCRQCDKSFSSSHSLCRHNRIKHKGIRKVYACSHCPDSRRTFTKRLMLERHIQLMHGIKDPDVKELSDDAGDVTNDEEEEAEIKEDAKVPSPKRKLEEPVLEFRPPRGAITQPLKKLKINVFKVHKCAVCGFTTENLLQFHEHIPQHRSDGSSHQCRECGLCYTSHGSLARHLFIVHKLKEPQPVSKQNGAGEDSQQENKPSPEDEAAEGAASDRKCKVCAKTFETEAALNTHMRTHGMAFIKSKRMSSAEK\n+>sp|P58006|SESN1_MOUSE Sestrin-1 OS=Mus musculus GN=Sesn1 PE=1 SV=3\n+MRLAAASNEAYAASLAVSELLSCHQCGGDRGQDEELGIRIPRPLGHGPSRFIPEKEMLQVGSEDAQMHALFADSFAALGRLDNITLVMVFHPQYLESFLKTQHYLLQMDGPLPLHYRHYIGIMAAARHQCSYLVNLHVSDFLHVGGDPKWLNGLENAPQKLQNLGELNKVLAHRPWLITKEHIEGLLKAEEHSWSLAELVHAVVLLTHYHSLASFTFGCGISPEIHCDGGHTFRPPSVSNYCICDITNGNHSVDEMQVNSAGNASVSDSFFEVEALMEKMRQLQECREEEEASQEEMASRFEMEKRESMFVFSSDDDEVTPARDVSRHFEDTSYGYKDFSRHGMHVPTFRVQDYCWEDHGYSLVNRLYPDVGQLIDEKFHIAYNLTYNTMAMHKDVDTSMLRRAIWNYIHCMFGIRYDDYDYGEINQLLDRSFKVYIKTVVCTPEKVTKRMYDSFWRQFKHSEKVHVNLLLIEARMQAELLYALRAITRYMT\n+>tr|A0A1B0GSE5|A0A1B0GSE5_MOUSE Ubiquitin carboxyl-terminal hydrolase CYLD OS=Mus musculus GN=Cyld PE=1 SV=1\n+MSSGLWSQEKVTSPYWEERIFYLLLQECSVTDKQTQKLLKVPKGSIGQYIQDRSVGHSRVPSTKGKKNQIGLKILEQPHAVLFVDEKDVVEINEKFTELLLAITNCEERLSLFRNRLRLSKGLQVDVGSPVKVQLRSGEEKFPGVVRFRGPLLAERTVSGIFFGVELLEEGRGQGFTDGVYQGKQLFQCDEDCGVFVALDKLELIEDDDNGLESDFAGPGDTMQVEPPPLEINSRVSLKVGESTESGTVIFCDVLPGKESLGYFVGVDMDNPIGNWDGRFDGVQLCSFASVESTILLHINDIIPDSVTQERRPPKLAFMSRGVGDKGSSSHNKPKVTGSTSDPGSRNRSELFYTLNGSSVDSQQSKSKNPWYIDEAFGGYLSEVVEENTPPKMEKEGLEIMIGKKKGIQGHYNSCYLDSTLFCLFAFSSALDTVLLRPKEKNDIEYYSETQELLRTEIVNPLRIYGYVCATKIMKLRKILEKVEAASGFTSEEKDPEEFLNILFHDILRVEPLLKIRSAGQKVQDCNFYQIFMEKNEKVGVPTIQQLLEWSFINSNLKFAEAPSCLIIQMPRFGKDFKLFKKIFPSLELNITDLLEDTPRQCRICGGLAMYECRECYDDPDISAGKIKQFCKTCSTQVHLHPRRLNHSYHPVSLPKDLPDWDWRHGCIPCQKMELFAVLCIETSHYVAFVKYGKDDSAWLFFDSMADRDGGQNGFNIPQVTPCPEVGEYLKMSLEDLHSLDSRRIQGCARRLLCDAYMCMYQSPTMSLYK\n+>sp|Q60880|OL141_MOUSE Olfactory receptor 141 OS=Mus musculus GN=Olfr141 PE=3 SV=2\n+MRNITEATFFVLKGLTDNNELQIILFLLFLAIYIFTLIGNVGLIILVVGDSQLHNPMYCFLSVLSSVDACYSTDITPNMLVGFMSKSKIISFYGCATQMFLAVTFGTTECFLLAAMAYDRYVAIHDPLLYAVSMSPRVYIPLIIASYAGGIVHAIIHTVATFSLSFCRSNEVKHIFCDIPPLLAISCSETYVNELLLFFFVSFIELVTILIVLVSYAFILLSILKMNSSEGRRKVFSTCGAHLTAVSIYYGTILFMYVRPSSNYSLEHDMIVSTFYTIGIPMLNPIIYSLRNKDVKEAMKRVLRKKINIKHRIKKLNDFSVFLMP\n+>tr|L7N477|L7N477_MOUSE Killer cell lectin-like receptor subfamily C, member 3 OS=Mus musculus GN=Klrc3 PE=4 SV=1\n+MSHLLGTEQASEPRKATKKTQAQLRFSNAAGDRLLEFSLQHASQKHLKASRHGYCKNFASPPEKLIAGILGTIWFTLLIALVISTRIVSPSQTYALCPKEWILYSHNCYYIGMERKSWNDSLVSCISKNCSLLYIDSEEEQDFLQSLSLVSWTGILRKGRGQPWVWKKDSTFKPKIAEILHDECNCAMMSASGLTADSCTTLHPYLCKCKFPI\n+>tr|J3QMI4|J3QMI4_MOUSE Calcium homeostasis modulator 3 OS=Mus musculus GN=Calhm3 PE=4 SV=1\n+MDRFRMLFQHLQSSSESVMNGICLLLAAVTVKIYSSLDFNCPCLERYNALYGLGLLLTPPLALFLCGLLVNRQSVLMVEEWRRPAGHRRKDLGIIRYMCSSVLQRALAAPLVWILLALLDGKCFVCAFSNSVDPEKFLDFANMTPRQVQLFLAKVPCKEDELVKNSPARKAVSRYLRCLSQAIGWSITLLVIVVAFLARCLRPCFDQTVFLQRRYWSNYMDLEQKLFDETCCEHARDFAHRCVLHFFANMQSELRALGLRRDPAGGIPESQESSEPPELREDRDSGNGKAHLRAISSREQVDQLLSTWYSSKPPLDLAASPRRWGPGLNHRAPIAAPGTKLCHQLNV\n+>sp|B1AZ99|OTUD3_MOUSE OTU domain-containing protein 3 OS=Mus musculus GN=Otud3 PE=1 SV=1\n+MSRKQAAKSRPGSGGRRAEAERKRDERAARRALAKERRNRPDPGGSGCEEEFVSFANQLQALGLKLREVPGDGNCLFRALGDQLEGHSRNHLKHRQETVDYMIRQREDFEPFVEDDIPFEKHVASLSKPGTFAGNDAIVAFARNHQLNVVIHQLNAPLWQIRGTDKGSTRELHIAYRYGEHYDSVRRINDNSEAPAHLLTDFQMLHQDGANKKEKMKTKGVDVKDGLRDDVEDAVHKVGSATGCTDFNLIVQNLEAENYNIKSAITALLQVNQGTGNDAEENHEPGDRVKQRGPSREEAGSGRRLSGNQGRNEGRMETSEARASPAEESKAHKSQLPKVTNKQRREQQRLEKKKRQEERHRLKALENRNGSRDTGRSEADMNTQVTLVKTFAALNI\n'
b
diff -r e34bdac5b157 -r 1320693cbf1e test-data/test.mgf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.mgf Mon Feb 11 17:30:46 2019 -0500
b
@@ -0,0 +1,209 @@
+COM=Conversion to mascot generic
+CHARGE=2+ and 3+
+BEGIN IONS
+PEPMASS=356.204468
+CHARGE=2+
+SCANS=949
+TITLE=Mo_Tai_iTRAQ_f8.00949.00949.2
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+688.612488 3475.960205
+END IONS
b
diff -r e34bdac5b157 -r 1320693cbf1e test-data/test_id.mzid
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_id.mzid Mon Feb 11 17:30:46 2019 -0500
b
b'@@ -0,0 +1,392 @@\n+<?xml version="1.0" encoding="UTF-8"?>\n+<MzIdentML id="PeptideShaker v1.16.9" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" version="1.1.0" creationDate="2018-01-19T02:00:07">\n+\t<cvList>\n+\t\t<cv id="PSI-MS" uri="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo" fullName="PSI-MS"/>\n+\t\t<cv id="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" fullName="UNIMOD"/>\n+\t\t<cv id="UO" uri="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo" fullName="UNIT-ONTOLOGY"/>\n+\t\t<cv id="PRIDE" uri="https://github.com/PRIDE-Utilities/pride-ontology/blob/master/pride_cv.obo" fullName="PRIDE"/>\n+\t</cvList>\n+\t<AnalysisSoftwareList>\n+\t\t<AnalysisSoftware name="PeptideShaker" version="1.16.9" id="ID_software" uri="http://compomics.github.io/projects/peptide-shaker.html">\n+\t\t\t<ContactRole contact_ref="PS_DEV">\n+\t\t\t\t<Role>\n+\t\t\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1001267" name="software vendor"/>\n+\t\t\t\t</Role>\n+\t\t\t</ContactRole>\n+\t\t\t<SoftwareName>\n+\t\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1002458" name="PeptideShaker"/>\n+\t\t\t</SoftwareName>\n+\t\t\t<Customizations>No customisations</Customizations>\n+\t\t</AnalysisSoftware>\n+\t</AnalysisSoftwareList>\n+\t<Provider id="PROVIDER">\n+\t\t<ContactRole contact_ref="PROVIDER">\n+\t\t\t<Role>\n+\t\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1001271" name="researcher"/>\n+\t\t\t</Role>\n+\t\t</ContactRole>\n+\t</Provider>\n+\t<AuditCollection>\n+\t\t<Person firstName="Proteomics" lastName="Galaxy" id="PROVIDER">\n+\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1000587" name="contact address" value="galaxyp@umn.edu"/>\n+\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1000589" name="contact email" value="galaxyp@umn.edu"/>\n+\t\t\t<Affiliation organization_ref="ORG_DOC_OWNER"/>\n+\t\t</Person>\n+\t\t<Organization name="University of Minnesota" id="ORG_DOC_OWNER">\n+\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1000586" name="contact name" value="University of Minnesota"/>\n+\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1000587" name="contact address" value="Minneapolis, MN 55455, Vereinigte Staaten"/>\n+\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1000589" name="contact email" value="galaxyp@umn.edu"/>\n+\t\t</Organization>\n+\t\t<Organization name="PeptideShaker developers" id="PS_DEV">\n+\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1000586" name="contact name" value="PeptideShaker developers"/>\n+\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1000587" name="contact address" value="Proteomics Unit, Building for Basic Biology, University of Bergen, Jonas Liesvei 91, N-5009 Bergen, Norway"/>\n+\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1000588" name="contact URL" value="http://compomics.github.io/projects/peptide-shaker.html"/>\n+\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1000589" name="contact email" value="peptide-shaker@googlegroups.com"/>\n+\t\t</Organization>\n+\t</AuditCollection>\n+\t<SequenceCollection></SequenceCollection>\n+\t<AnalysisCollection>\n+\t\t<SpectrumIdentification spectrumIdentificationList_ref="SIL_1" spectrumIdentificationProtocol_ref="SearchProtocol_1" id="SpecIdent_1">\n+\t\t\t<InputSpectra spectraData_ref="Mascot formatted MGF of data 13.mgf"/>\n+\t\t\t<InputSpectra spectraData_ref="Mascot formatted MGF of data 8.mgf"/>\n+\t\t\t<InputSpectra spectraData_ref="Mascot formatted MGF of data 7.mgf"/>\n+\t\t\t<InputSpectra spectraData_ref="Mascot formatted MGF of data 6.mgf"/>\n+\t\t\t<InputSpectra spectraData_ref="Mascot formatted MGF of data 12.mgf"/>\n+\t\t\t<InputSpectra spectraData_ref="Mascot formatted MGF of data 14.mgf"/>\n+\t\t\t<InputSpectra spectraData_ref="Mascot formatted MGF of data 11.mgf"/>\n+\t\t\t<InputSpectra spectraData_ref="Mascot formatted MGF of data 10.mgf"/>\n+\t\t\t<InputSpectra spectraData_ref="Mascot formatted MGF of data 9.mgf"/>\n+\t\t\t<SearchDatabaseRef searchDatabase_ref="SearchDB_1"/>\n+\t\t</SpectrumIdentification>\n+\t\t<ProteinDetection proteinDetectionProtocol_ref="Pept'..b'tionHypothesis id="PAG_0_1" dBSequence_ref="P27048" passThreshold="true">\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_5247">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_27936_1"/>\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_35350_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_11948">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_28486_1"/>\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_32857_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_38645">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_28823_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_64667">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_40692_1"/>\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_46888_1"/>\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_49545_1"/>\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_59118_1"/>\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_62451_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_68343">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_41960_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1002403" name="group representative"/>\n+\t\t\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1002401" name="leading protein"/>\n+\t\t\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1001093" name="sequence coverage" value="0.0649"/>\n+\t\t\t\t</ProteinDetectionHypothesis>\n+\t\t\t\t<ProteinDetectionHypothesis id="PAG_0_2" dBSequence_ref="P63163" passThreshold="true">\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_5248">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_27936_1"/>\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_35350_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_11949">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_28486_1"/>\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_32857_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_38646">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_28823_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_64668">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_40692_1"/>\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_46888_1"/>\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_49545_1"/>\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_59118_1"/>\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_62451_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<PeptideHypothesis peptideEvidence_ref="PepEv_68344">\n+\t\t\t\t\t\t<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_41960_1"/>\n+\t\t\t\t\t</PeptideHypothesis>\n+\t\t\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1002401" name="leading protein"/>\n+\t\t\t\t</ProteinDetectionHypothesis>\n+\t\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1002470" name="PeptideShaker protein group score" value="62.4192"/>\n+\t\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1002471" name="PeptideShaker protein group confidence" value="99.9665"/>\n+\t\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1002542" name="PeptideShaker protein confidence type" value="Confident"/>\n+\t\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1002415" name="protein group passes threshold" value="true"/>\n+\t\t\t</ProteinAmbiguityGroup>\n+\t\t\t\n+\t\t\t<cvParam cvRef="PSI-MS" accession="MS:1002404" name="count of identified proteins" value="3290"/>\n+\t\t</ProteinDetectionList>\n+\t</AnalysisData>\n+</DataCollection>\n+</MzIdentML>\n\\ No newline at end of file\n'