<MzIdentML id="" version="1.1.0"
  xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 ../../schema/mzIdentML1.1.0.xsd"
  xmlns="http://psidev.info/psi/pi/mzIdentML/1.1"
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" creationDate="2011-03-25T13:16:49">
  <cvList>
    <cv id="PSI-MS" fullName="Proteomics Standards Initiative Mass Spectrometry Vocabularies"
      uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"
  ...
</MzIdentML>

<AdditionalSearchParams>
  <userParam name="Mascot Instrument Name" value="Default"/>
  <cvParam accession="MS:1001211" name="parent mass type mono" cvRef="PSI-MS"/>
  <cvParam accession="MS:1001108" name="param: a ion" cvRef="PSI-MS"/>
  <cvParam accession="MS:1001146" name="param: a ion-NH3" cvRef="PSI-MS"/>
  <cvParam accession="MS:1001118" name="param: b ion" cvRef="PSI-MS"/>
  <cvParam accession="MS:1001149" name="param: b ion-NH3" cvRef="PSI-MS"/>
  ...
</AdditionalSearchParams>

Path /MzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/AdditionalSearchParams
MAY supply a *child* term of MS:1001302 (search engine specific input parameter) one or more times
  e.g.: MS:1001005 (Sequest:CleavesAt) 
  e.g.: MS:1001007 (Sequest:OutputLines) 
  e.g.: MS:1001009 (Sequest:DescriptionLines) 
  e.g.: MS:1001026 (Sequest:NormalizeXCorrValues) 
  e.g.: MS:1001028 (Sequest:SequenceHeaderFilter) 
  e.g.: MS:1001032 (Sequest:SequencePartialFilter) 
  e.g.: MS:1001037 (Sequest:ShowFragmentIons) 
  e.g.: MS:1001038 (Sequest:Consensus) 
  e.g.: MS:1001042 (Sequest:LimitTo) 
  e.g.: MS:1001046 (Sequest:sort_by_dCn) 
  et al.
MAY supply a *child* term of MS:1001066 (ions series considered in search) one or more times
  e.g.: MS:1001108 (param: a ion) 
  e.g.: MS:1001118 (param: b ion) 
  e.g.: MS:1001119 (param: c ion) 
  e.g.: MS:1001146 (param: a ion-NH3) 
  e.g.: MS:1001148 (param: a ion-H2O) 
  e.g.: MS:1001149 (param: b ion-NH3) 
  e.g.: MS:1001150 (param: b ion-H2O) 
  e.g.: MS:1001151 (param: y ion-NH3) 
  e.g.: MS:1001152 (param: y ion-H2O) 
  e.g.: MS:1001257 (param: v ion) 
  et al.
MAY supply a *child* term of MS:1001210 (mass type settings) one or more times
  e.g.: MS:1001211 (parent mass type mono) 
  e.g.: MS:1001212 (parent mass type average) 
  e.g.: MS:1001255 (fragment mass type average) 
  e.g.: MS:1001256 (fragment mass type mono) 

<cvParam accession="MS:1001211" name="parent mass type mono" cvRef="PSI-MS"/>
<cvParam accession="MS:1001108" name="param: a ion" cvRef="PSI-MS"/>
<cvParam accession="MS:1001146" name="param: a ion-NH3" cvRef="PSI-MS"/>
<cvParam accession="MS:1001118" name="param: b ion" cvRef="PSI-MS"/>
<cvParam accession="MS:1001149" name="param: b ion-NH3" cvRef="PSI-MS"/>
<cvParam accession="MS:1001262" name="param: y ion" cvRef="PSI-MS"/>
<cvParam accession="MS:1001151" name="param: y ion-NH3" cvRef="PSI-MS"/>
<cvParam accession="MS:1001256" cvRef="PSI-MS" name="fragment mass type mono"/>

<userParam name="Mascot Instrument Name" value="Default"/>

<Affiliation organization_ref="ORG_DOC_OWNER"/>

<AmbiguousResidue code="X">
  <cvParam accession="MS:1001360" name="alternate single letter codes" cvRef="PSI-MS"
    value="A C D E F G H I K L M N O P Q R S T U V W Y"/>
</AmbiguousResidue>

Path /MzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/MassTable/AmbiguousResidue
MAY supply a *child* term of MS:1001359 (ambiguous residues) one or more times
  e.g.: MS:1001360 (alternate single letter codes) 
  e.g.: MS:1001361 (alternate mass) 

<cvParam accession="MS:1001360" name="alternate single letter codes" cvRef="PSI-MS"

<AnalysisCollection>
  <SpectrumIdentification id="SI" spectrumIdentificationProtocol_ref="SIP"
    spectrumIdentificationList_ref="SIL_1" activityDate="2011-03-24T11:37:37">
    <InputSpectra spectraData_ref="SD_1"/>
    <SearchDatabaseRef searchDatabase_ref="SDB_NeoProt_tripledecoy"/>
  </SpectrumIdentification>
  <ProteinDetection id="PD_1" proteinDetectionProtocol_ref="PDP_MascotParser_1"
  ...
</AnalysisCollection>

<AnalysisData>
<SpectrumIdentificationList id="SII_LIST_1" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
    <FragmentationTable>
        <Measure id="Measure_MZ">
            <cvParam accession="MS:1001225" cvRef="PSI-MS" unitCvRef="PSI-MS" unitName="m/z" unitAccession="MS:1000040" name="product ion m/z"/>
        </Measure>
        <Measure id="Measure_Int">
  ...
</AnalysisData>

<AnalysisParams>
  <cvParam accession="MS:1001316" name="mascot:SigThreshold" cvRef="PSI-MS" value="0.05"/>
  <cvParam accession="MS:1001317" name="mascot:MaxProteinHits" cvRef="PSI-MS" value="Auto"/>
  <cvParam accession="MS:1001318" name="mascot:ProteinScoringMethod" cvRef="PSI-MS"
    value="MudPIT"/>
  <cvParam accession="MS:1001319" name="mascot:MinMSMSThreshold" cvRef="PSI-MS" value="0"/>
  <cvParam accession="MS:1001320" name="mascot:ShowHomologousProteinsWithSamePeptides"
  ...
</AnalysisParams>

Path /MzIdentML/AnalysisProtocolCollection/ProteinDetectionProtocol/AnalysisParams
MAY supply a *child* term of MS:1001302 (search engine specific input parameter) one or more times
  e.g.: MS:1001005 (Sequest:CleavesAt) 
  e.g.: MS:1001007 (Sequest:OutputLines) 
  e.g.: MS:1001009 (Sequest:DescriptionLines) 
  e.g.: MS:1001026 (Sequest:NormalizeXCorrValues) 
  e.g.: MS:1001028 (Sequest:SequenceHeaderFilter) 
  e.g.: MS:1001032 (Sequest:SequencePartialFilter) 
  e.g.: MS:1001037 (Sequest:ShowFragmentIons) 
  e.g.: MS:1001038 (Sequest:Consensus) 
  e.g.: MS:1001042 (Sequest:LimitTo) 
  e.g.: MS:1001046 (Sequest:sort_by_dCn) 
  et al.
MAY supply a *child* term of MS:1001194 (quality estimation with decoy database) one or more times

<cvParam accession="MS:1001316" name="mascot:SigThreshold" cvRef="PSI-MS" value="0.05"/>
<cvParam accession="MS:1001317" name="mascot:MaxProteinHits" cvRef="PSI-MS" value="Auto"/>
<cvParam accession="MS:1001318" name="mascot:ProteinScoringMethod" cvRef="PSI-MS"
<cvParam accession="MS:1001319" name="mascot:MinMSMSThreshold" cvRef="PSI-MS" value="0"/>
<cvParam accession="MS:1001320" name="mascot:ShowHomologousProteinsWithSamePeptides"
<cvParam accession="MS:1001321" name="mascot:ShowHomologousProteinsWithSubsetOfPeptides"
<cvParam accession="MS:1001322" name="mascot:RequireBoldRed" cvRef="PSI-MS" value="0"/>
<cvParam accession="MS:1001323" name="mascot:UseUnigeneClustering" cvRef="PSI-MS"
<cvParam accession="MS:1001324" name="mascot:IncludeErrorTolerantMatches" cvRef="PSI-MS"
<cvParam accession="MS:1001325" name="mascot:ShowDecoyMatches" cvRef="PSI-MS" value="0"/>

<AnalysisProtocolCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
    <SpectrumIdentificationProtocol analysisSoftware_ref="ID_software" id="SearchProtocol_1">
        <SearchType>
            <cvParam accession="MS:1001083" cvRef="PSI-MS" name="ms-ms search"/>
        </SearchType>
        <AdditionalSearchParams>
            <cvParam accession="MS:1001211" cvRef="PSI-MS" name="parent mass type mono"/>
  ...
</AnalysisProtocolCollection>

<AnalysisSoftware id="AS_mascot_server" name="Mascot Server" version="2.3.02"
  uri="http://www.matrixscience.com/search_form_select.html">
  <ContactRole contact_ref="ORG_MSL">
    <Role>
      <cvParam accession="MS:1001267" name="software vendor" cvRef="PSI-MS"/>
    </Role>
  </ContactRole>
  ...
</AnalysisSoftware>

<AnalysisSoftwareList>
  <AnalysisSoftware id="AS_mascot_server" name="Mascot Server" version="2.3.02"
    uri="http://www.matrixscience.com/search_form_select.html">
    <ContactRole contact_ref="ORG_MSL">
      <Role>
        <cvParam accession="MS:1001267" name="software vendor" cvRef="PSI-MS"/>
      </Role>
  ...
</AnalysisSoftwareList>

<AuditCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
    <Person firstName="firstname" lastName="secondName" id="PERSON_DOC_OWNER">
        <Affiliation organization_ref="ORG_DOC_OWNER"/>
    </Person>
    <Organization name="myworkplace" id="ORG_DOC_OWNER"/>
</AuditCollection>

<BibliographicReference
  authors="David N. Perkins, Darryl J. C. Pappin, David M. Creasy, John S. Cottrell" editor=""
  id="10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2"
  name="Probability-based protein identification by searching sequence databases using mass spectrometry data"
  issue="18" pages="3551-3567" publication="Electrophoresis" volume="20" year="1999"
  publisher="Wiley VCH"
  title="Probability-based protein identification by searching sequence databases using mass spectrometry data"
  ...
</BibliographicReference>

<ContactRole contact_ref="PERSON_DOC_OWNER">
  <Role>
    <cvParam accession="MS:1001271" name="researcher" cvRef="PSI-MS"/>
  </Role>
</ContactRole>

<Customizations> No customisations </Customizations>

<DBSequence id="DBSeq_1_Rnd2psu|NC_LIV_080090" length="16207"
  searchDatabase_ref="SDB_NeoProt_tripledecoy" accession="Rnd2psu|NC_LIV_080090">
  <Seq>DPARMTSRLSEAAPAEESMSAEATFHWYSPMLEYARAAPLWLPSRMLIEHAKPGKREGDSGHLESEATAGPPSPPAPPPEATSLPSYRGLLAFSQASPPLCPVQLYPPRRRAHFELPLVSSDESQESRCLATCLRGVGLSWDYISPAGTSLVVAEPHGFSGPDLIQGPSADTARAELVPFFSAWSLEERVQSVSWGRRYARRRPVIRRRCHNAAGKGPKRLGRRQRKELGSREPVRAGPGFLPEDLGPAQSARDRLVWNDHSPAVDTAMSDAASPNEAGSGPWAVPEPESPALFLFEWAVRHLQPEVEPVNKSIIRESTLATSGAQEANRRVRLADVTLEGSPVADLCMGERMAGAGQAQFAVSCVLEFVFGLSQDAEEKRNEALPDPRMVGSAAFACLAAAQWERLLPKTYEAATFFYLQVILDAPAPIRSPIRPTLDPRTIPVNRRARGVAPQESFARGACEGTGEHPSAALWAPFRQAPTSDTEACAAELQESYGAQDDFYNPLELAGDRAPTSTLGFYLEFEPVEGPDAGNRTMESSEAAYAEAPAAGEADTLRLSSRAESGLPTSAWESASSATPLHEEMESVEEARNRRFERSLNRRRWFDEQAESPLAFSYSQNCSQVDSPGRSRQTELFQLTGVGLSVARSNHFSKTEIDNEGREPPLLFAPRLERLSESLKQRTECPISEQSAASTGSVGPQLSARASEVFAVALAAIIPGAIDFAREELGGRFMLLEFLASTSPALAASAKRTNRSVFRTPAPADCNTEVFRVAVRRNGGRSFKSMASYVARLMLTLSDDEVVRQSSAAGCDILEHEEGRMIIILLCGEYSSTNEESHMTRPAAAQIIIGLQPPFRPRVLPPDTKRDSGYIGFAASGMCVASFGLSTEDPAEGMLDPDEPADGVEGFRRAWLQAVKCQANGPGLRLLTSEGASAQREPRPPQPRDTLVWLGFLMCQRRLLDPSFLTLFRLRQAAVDFERLLPFVTPPAPNTSAAASALGLTSAGPRGRHQVDFVSATSQTAAQTLHSSPDRCGTHRLLWAEQVLAQSELVIGTGAHVERTLPDQTHLGLNLYPVVRPRSEAGSGAPRRRLTRRVQPFLRVRAERSLRGDPALANFSRTQRVSRAGLEQASGLVEDHGSANVFQECRASTGAREQMRRSHTRLASLEPSIRQYARFDYVAVTLRRPRRASMPSSSAEFQTAGRSASGRNPQRIEDDFASLLESGTVRRVRENEGEVEAPESGRERVSLSQDTLVYLIDSREDSLARYAATGEGNGPVEDTPNETVYVDLGPIQGFPLLEEQREVEPTSLFAAWQTVAVLEAQSRRRSRTRVISWSLCAQPEFFWWTGRLSHRHGTHLPDGQCERETCLVFDPTGRSRMAQGAEVLQANPSDNAPGWVVGASVRDDFATLDPFSPCPGLQTPQAAESARATEAVTGGLEGAEQAEPAASGCSEYLPRLPRGLDTIPPLSPPVGRLTRPRVTGSGALPERLSLPTLCGQLHAPSRVSGHGAPERGDPRTLRSTRRGVNYNPRGALPRWSRETCAQRAPLGSARSCVLEDRGARRNRESGARVVSVDVMGHLTATADVKSGLIGGGITQGEPFRSRPGSALESDAMLAYMLVNGAPAVSQRGRGRSPPPGCRARQLGAPMFPSNGIMFLVSKAVSCLVEYRGDRGDRVLEASVRVVATRPLFGSVGAESGLWAKGVESVAKEALRRSVGTVQARAGYDTGERPFEFSLRSELLDELLVLSQRDGRQCREARVTLLVRRNAVICRRRQRVEDGRAAGSVISRRAGWGHRSYIRCLEAKRELLGLVLGAEMVGDEGGSFDVKGSALSTRLPNESIQFRVVLDALEPFANDTILRVHLSELGPLGLIAEYPDPRIAPDVHNRSAEETLREERLSIPPVDSDAKAPALQGVDSSMSIERLDEKTKIVRSERGLLRVGATVHASAVPVASRGGASSRLSRDADLSPRRFAAISEDQKLSADDAVVPAVQDAGLHTEIGFKGQAGLEESYRNSLDGCILFGARRGSLDSSDKQRTCALTDFYKAPLVQDRLDHRLSSATEDTFAQPYANLLSTSTRFVGTFIKGTEAERVGKKSILFDAAPGPESSPRLELESLSGIVFGLSGLRLGFVSMPLSPAPPSDKTGSSPVGCADVAPEIALPRPDHRGPLEPDGCRVDTLRTDDASSSVPESATPPCERVTTEGLDGPAPATASASSLRPISSNGAPRVELSQGLASRRNERTAASTEQDTLPSHQIAALPDGREMDAGRPRAAGGGTLRGEAIGPRSRRFGHHAELSHAVVFCMRDLQDQPGCVNVGASKQSANSFGQREEDRAIEAGANLLAKAAAAEALVGALFPALHYEPEPAGGEVSFSDCLGSSSEYSLSYHALRRLFLSKEKARDAVPCHATEVSVLEATMENAVPNQAMLALDCDDQNGAPAVPALERGLPCGPEREDRRVRPATLPDAEVAEFRQKEQFQTLAPRPWQEEQLESTFWLDRLLGEAANASYEVAVDEEAEAMTPPLELLREVRLIELWTLPPSDEVSLVRGSPEQVQARCCRYLAGPGGRQELDAFRRTAFDPEFQSALRSALPDHAQAQRQGREVIRPFRRFLGAALSEGRRSELDLSINHKGALSKRKDGGERRLHFSSIGRHARAHDRAQPTHRRDKEGRADDRVLEVVAISTVDYLGGRHREVSSHLVGPRAYIHSRRTGEPEPPRVGFWIEGSSTIPSVRVVTAGRPPGDNCTAGREWAPARVARRVSPEPARGHWLASLALKWCSSGVPLTPAPALLPAFEDPRRRGSPATQASSRPARMKTTVDLAGCDESVSSEDDLALLVHDSGTTPHPAEFDESEGASECSGTRSRAKSENRSGFRIDKVLAISGAVALKHRKSGESEMACPSYVEADHVFRSWRLVESSMREGARADVSAAEGTPRHLMSNARQALADAFIYATSASQALILPLEVNDQSLRTERRARTAVHDSTCLSGLAYEFQMGVQQLEDSSSPPELYGLGLMDGERGEEEGAWMKIFAYGETALENPEDSPEMDAGAWLRDDRERSRPRLPLRRRSPPTNSPSEYGQLVLWAVSVVAGRDAFRAVESGGPSSALMDRRGFEYITEATASSDAVPGLRTRPRLRVIVRPAQRSPRPEEVEAEAGSQENPRSGLADDVESLSLAERVFLSALTVLAEPLASREFWVQDCESQDGEPQAADAQRMGVFTILRGDGEARSKLKETPRAGSTACSSLLVGRSEELTSDKADDLLARNAPKLKLRSAKLGDDTLAGAIPATELTNRGFLVWDRKLIRELELPVTSSLAAESSSDTHSAGLTFDSEIPGHHPNGPPGICDRCTPLVSDTFGASAIEASRPAVTGVLESALRPIGVNPCHRETEPSSRSSPQEPELADPMVQFPAEGSAETPSAAVAPAVDEARAMATGCSEARREVEASWATEENNLAGPPHAPLALADILDLVHGVHGPSNMGSQVGYVWRGFEPVQTLYREVEGSQFDGGGRSYGVKAEVEGDERSTHLPSDRSADPPGVPFAVVEISGFLRSSVAVGLSQQPLSALEGLGASLHMAGVSLETSGETQYSSPRGKGLVAFIKGISLGISCRSPSAVRPPVSATVFNWAVPEPAAIPGPEFVPLPALSPAPSEEPAPLGPPSRVAPRMTQYLERGSHMCGRVYFQKSVDRLQLGRTSFEGPAARSSVRPCCATSAKPGILRRLEKAHSAEQSAARCYPDAFHCRKKFRFQSFRPNPSMPNMQRTAGYFSSLGNLEGRAMFKPLSSMILLDDPNCFAKQLASLGQAIVLATSRLRSVLALSSEAAWQQADLYNVSLISKRLRRELGVVEDYATSVANLLIDAVHDARRPRLTRRRDAKRQPPLDEALDSVITLLRGSHSLDSILASSERDARGFSSSGASFQGARKVSKSIASPSVTPALAPRGTLVAFGRVGRPWSAELWLPEGPELLESDVLLPTEAPFQPIETCDLSGVHLEPGLGAGGNLLCQQANADHPLQPVMLSVEAPGTSGEYSAWDTLGATTDVCRGSDYFPALPELPPAESWPCQPGQAASLVTGSERAFNAPILVHGLGAIIAERGIRIASCTASGTKQPKLRKIKTTSPFASTGPLIIRVRRRLEADAEQALGAQSDRRELRHFSENQAAGNCDNRREQESDLPKRQGREPAGSPPFALDDLFPEDLIDEQREFAGFGAEQARRTAPRPDATRHMKVRADSPARTLVTAVLGTPPVFAGFRRRPSDDTHGSGGWREERPPAQDLGATLSPEYRLRRQPESDRELLLRAGPNHPDRSTDPQDSAPPRVAPPVANDSYGTQWGSDEAPTVEHGRIDGRRGPGSPDSRFTVLRSLSPGVSLVAHEDDPAQAPDQKASNRLYRKDAGLSAQSFLFGNVDEYMARFFQDLKEGQFSVKPPGTLTWRFGPYAEARSTATVGPEEASEILAAPNCTLAAQAPEGERPGKPLSPSRITAASRAAEAFNYFSSLWLFPPSQESSAVLSRIQFSLHRHRTRRFRGLMQHVEQKKKFSTTTFLDRRSLEAHQSYSDGVPANSAVRRGSVGASWHEGQERTDRFPDSWSGHGTCVEVLLGAQGPFRRREHEGLFSRPVLLARLRYDPTDTQAGPPPSAADGDGQPVSGALPGIWFESHNILEPQIRRCPEERARYMASTFVPNPDSDLAVSLAAALHEPGAELLRSQRAPRAGDFQRQRQCQGTEQRDDHASGPTPVLPCVEALQLLNHGRLYSEAQENGCPSDSDEQKLSMWNVEKAGEPKGDVYSPNLRDYAPGVSDAVQAQKRIEAQKIPRASDSHNTRHPLGHLSFCRVNDWRHRVNRDNVRDEISVSRLRAQQTTKRVSRSLPEAEAALSGAFAEQGAHDQGRATNATLRLSEAQFSAPGRRNPTPTPRRRLMHYPYSLANGVIIGDTWTSVEGLIAGAYNGMLGYATGAARRLLRESVYPLPRAVKSVQDRGGWMQSGSIAAEVLAFRALAGAQADMSVFLSIAIRGAASQEWWPAARGLLALNVENYPAAPRITANPGRLFSECSSQGTDLASRKAFRAQRLPRGRSLNRSEDGPSRDAWSGTSPTYTAGKTDDRFQEIQTSTGVSGDSKELLALAADARRPRPSPSNAGREADFQVSDKERRKAEVTRVRSDSLAACDALARRQALMSMGLIQEQTFEYVALLGPSLPPCPFLSPGPWAAVDGRVGELASDTLANVAKRVPLPGGVARSVGIPATPTPCCPMQFYDANSRLFQILAFGGELSNDTSGSSQPTSERGPLQLCSCSGFRAALDVPAKIPPAHPVFLDFLQGIIEVCELGNMLQLAEVRSPLGPPEAPVPPGAEHCGGPYSSLEGTGMERIRYLPGIQPMHTCESFNERRVSQAWTASSQERACRSPSQAQGLYAAQDARQARSRRDVPVFGVELRIVGRESQDRRKRRRPKGHVPEFWHGMPLQSATQLLLEGRSYDVEQCGRRAVASRSGVGSGAKSRIMGERPCRTSYDKLVPVLSAWYIRLDAFNAISGLFELAISELIQFQGRGGSRGYAVNSDASDSMTFENFVESGAAALAYMNIPTTDPDPSLTSAEQVLQPSPLGARRRFPAHESGRAQEDCAEPRETHAYHFARPSDTRSAHRQVRLSHEDRGRLQTENGAMPTILSFNDCTEEMVRRRAESMSAEAPAPFLEGPSSPVPPLTSWAAAGLSCDLPSKPRLFPEPPLASSGAAELETQQLGCERLPYSTGEVSGRVQGAKVWKTRGTPSRRTVVLVPASDAVRSAQGTAAAQALETCSPEIDGMANRAALTVEPLFSASMPAETWKAKRRTDLRLTGPDAGPMERGPVSAGIWPIVLEPESARAAAPQPTQDPEDFRELEKPYLSVSKIACIWGAVQRREEAAEDKFAMTKWETALGLLESNTPMERGGKAGTSKVVAGPEVYHEAQLGRSGANKPWESPTPADSVLNGLAANKPSKSGTKNRTHEKDIVTEPALHPGVKTVAGTTAEEPEPAYERRKGLARAPRGGRCARPSRQVAASSRRADQRLAEAFVGRSLKALKRPSTQLDPGLAMRKRRSAARLAPCATIMFYCSSTESLASLEKEVLLGASDRDGAGASKVARDGRKASSEWRREFATAEDNSRGEESMSDSPSFGHIAPLPIDEDPDVPLSLVPHQCTISVELAPGPEASAPVGGREPLARVIPDMVGLSPPTMWLLPGQGAPSGPVELYAKYLQDSLGCEGDLYPADAQSMFELTRRRVAADGGGRANYLAYAVARSREAASGLGLVQSRFADSVRRNSVQSVLDERLAKRQLWAHRRRGPMFPSAGDRGARSASSPVDSNGLVVTGVAPRREASCDGCHPRSIQAVRVDTHWKLSEVSCPRRLVAGRAFLWCGLEAARSVPLRMDEEAHSSSETEFGSQLSLFLMCSEVQNLGSFRPSPSPSNGASEGAPNHVHSESCRAALAEPGLEYEGEFKWIGNRAKDRSGMQQTTGSTHNPCPIRVATQIVTVALSQSGSRVRLQSIRAESDLRADGQDEGDDAAVVPHFAFPLGEVGTPWLGSERGLHGAVYSRRASIECETPASNTARDGPINVRKKREIPYVSAEFNRGGAPRGARWLLGGLMSSHLGWPTALEERVARPFSSEIWPNTFAPYRLYDARVLPEVDPVRRPTKPRTQHRPIMPSCSTKSLRTSGSYRNSSGPRESPTSPGQTHPRVRAEPLRDSDGENGQAADSVPAGTRIPTGEAQPAERRPHRLFLLSSVRLGSEHLSECKTLSAHYVLDMSGRQMPDSDRRQGWEKQRASLIVLAGLGSKAAGGMCWNVNDPSQTGLSSFRATRAEESNFLSCTASFGASGIELGSRLVIERLCCAEGGAGWTLSQSKRAAVLEEGFLVQQLWRLANVKGWTFRATPRAPPARAERDRALLFEHTVKGRNERCSLEAMAKDSQAAEGLLHPGGAGAAPSNRRRAESAEPEPGAVRAHANEGFSLSEALKLGFMHIRGEELVFALDGSQHENEQLPYSPPEPPADSGPNRSQATAVRTTQKPEKGKDSNARLVAHRVLVVSADAQDAPDPCKTIKSSSERKKRVLISWRRRMELLLLSASEAYPVEFPEKQQLKKQKRNAPRRYQASELVTLEPAANGSVGPNGAADLIKLVYVQLDSSTHPGSELTTSRCRALETARQELLHEQVTREIIAADTERPQFPLRRPAAQRELEALAAAVGERHIPPPTLLVRAEACLYGARFGRDAERGSSPRRREFATAPGTAVVQCATAEGDGRYDSDVRQEEGNLVGAPNISGIEYDLPRGVPALFTWREAGVDCSQQSVVRDGQSYEFLTHSSLSHVGVAGSMADQERSDPYAQNEVEVAHSSQFLAERVTPVPASGASRLTGRDAQTLTSSLTVQPQVQLQAAVAVELEESTTDPAADHEAWEGFREQDVNHVKPLAASALLGRHQPFDPLCSAALMTILELGREGEASSQMLGALALVREDADEAGPRSPDAESVSRFAFPQGEAAIFSLLWGCTAVGAECADPELHHWLFFALGRPPLVARFALDTCLPDGVEGGFLNLCSHLSEENSGTSATDLAGASHFDFRFARAPSRPFDAVARVDGVDNFDRPMVRRRLILLRNMARRVAARTDLHGDQTTGRQSSRRELGATATVQGVAANAERGGWGSSRQQFRRSRDARDRGAEGGSPRASGCSEASEANLLCILSAQEGPCEVFLPLEALGEAVADPNYYSCNMDREDYSAATFDITALRLTPPCVRPIAETRLTPDNDERPGAGRSSMLSLNCAVFFRVCRSPQSVSLRVTSGGAVGGAESRRRAPRFRGLLTVLAYATPCRYSAAAVPAGREEVLSAILASTVRLLLELAASGDRGVSQMFRPNAFGPEAGAASEAMRQEEAEARIRRAAATAGFARGATFTYACRAPELVPSASGSRIERIGCSGPFLTERGCRFRPAPPNSRRVRSSTDMARESSIGCVSRLRASRDTLSLPVATESDNDSRQGECHEELRGSSRGTWEDAPPPHSLLMGMFLVASHTGLCDLAAAFWMVAFEFESSHLSSTLLRPEVRPCEGVESQRFADFPRFRGARGIFRRRREVPRPRLNDDGLLILSNALPPETRAAIAVEWEEANMANVRIVSSSASLLLELVTYAVGLTVTQTVPGWGLSRLGYGDASNIRIEEELRHSFLARYSEGEWLSTYAPPAGEARTGRSLPFLLPPAIRHPETATMSVALARFDIPATRDIQGASVGAGKDVESAELGPGYDSPEHAGLAMLAAIRFADRRARASRPARRRRIRKQRLRSARVELIDKWFWSNQGTTSLGALLQVSGSHLANDSSLKFSQHASEAASLRESAAWVSLDLDEPRMDIMRLRPEPRMTGQGARLYSGKLSVVAWFEGAEDSDATEETPTASGTNESEERSDLQGTDPASSDLARKLRSATTIKDLQSIPLAGSDTPDKQGSYVRSASTGVAELIRDQEHRGTKAESKEERAEDRYGLFGSWSAIRECTREPVESAMWPTLYIVTRAHAPLYTPGLEAEDPTPEQRWEASPQAAAIARLCGHGSCGGERLGRVPRERRGAGARRKQYSFQIASRRRVPRTFVVSHAAENKMSQSMGEGCHEAALSEATKIRRGDGGGITTDLARSKKPFGLPSKVRWFRREDGPCEASPQLSARYRDEAVASVTQLFQRIRGPQLTGRRSPCEAACLASSVERTPRMKAGDEDLSSEVSTSNARYNAPCEPEQCPESARLTEGGLRARRPDFNATNGATADETIAHIFTRVPQPAPLRPRDGAAAASPLRRSAVADVSSELEVERSEFAGANRENKNDRRNVKRFYYPSFTGREAAKVLGREPEGRAPVLRTYRGVRATCDVSFKLRSVQIASLKRGVVAKSSKPEDGEKDSQPPLGASVERGQTQPLQIFCEPEAAVAASADARADLRVNDGLDDEGDSSAGLPDSTTVPIVQTESLPQERITVFGSLYPATGATHLLMADRFPRAAKDIKSVVSLSQCGKARIGNAFESIAEITLGESGRSLGAVGRFRFMSASITASSIVSETKVRSETRKAKLVELVLTRSTTPWDRPISPAEPGFYSSVSPRVPSGSRRRSTLEARRITVALKKERDRTGRPMIKEFALASRRPAAENARKWWKPGWRKGCNYSEAARNERDVERHPKLVRERVPAQDTARAILEGESPGPRRVRRILRGRLASYVVRSEHMGAQTAGAGMPMGARTPSRLPGFLEPCADVLQSSRLVSLGPMQATRPRVECHYFEGEQDRWFIELLCPGRAPFAPPPPLGPASSGVVNVLGPSCPSAVLARVSRVSQSAWYPEGAKAEGQARGADGRACPGGLVQTDLEWEDLNGCDSLTADEQFQPPPFPGHGRLRRPLISTPRVMFARRPSGISKASRPQMLGATFTLESFALEPQDFFERDSVHASHRGQPAQKKEASAGSSHSGAVGCLYTAAVSRQFHATRRWETCRGSAVNLGRCSLALAVYPDTRSADLVLSDKLGWGTTKTERSPEGEKGIVSLFAILTTLCELAASPHSAGPTEDADSNAIWQPTERSKAATESGELNRSVAADYPLFASVENYLEGYFVGLGFLHGNLVRSELGRDASAFHHVAEDGRGRRSPLRSESNVKADPRMMEISSLSSLLEFPVRRKCDKRLGSHKVPDKMRGRQGTSRLLAEQTRGSVRAPEFRPSAIYAPALTGEAIQDLQALQDLFGSPGQSTQLAAPNHLQSRGVRLERERMVNPRTYASSGTSEVLEGHSAGLKSSELASFPLYAGEMPNCSGDRIWAQAACRAEWDHASHETSTTLEIEEALAPDIHNVSCPGLDRSLHAEDRLRPSFQRHGAGFSATLFKSQQGLHRRRGESMDLDEAQDSEWYEEGTEDSHASSNVLRLIARAGGRGQWRACADFGSENFGRNHVPCLPVGEGLSIVAQRSRERDLEDFRSHADSGLFGSGEELAHVLFDSRDAGVQEVDLRQVRETRFGDQDLTFEWSAESASADPNVLLELAVALSRFCAATELNNETAELDTRWPDAHPLDHIAADRSRGLLFMHSLLRGGAIAATVCRFRDDMRRRLIERESKVAWDLSGPHFRLAELLFACQVRPQPAELIRHYTDLLPLPGMLHAVVYHPRFQACEDHLPSGPEPAIEGDSLGSREVEEDPCDLQGADRSRARRDRRQPQYQSRPERLQSPRPRVPGTASRWNELSSQVVSSAEENQEKLCHPIGHYMVAQDLMRAPQRPCDRISRKLEATSAELFEDRPVENRRRGHKRRLCTVNDEESREAVHEQTDDERGARRSKANPSKVTVFRRREQRTNKMQDIELLEDSPMDSSARVWISRCSRITQTRPECSVRNSQAPAWEHLACSDFVGVGRPLLAPQTEPLSRLQSTTHPVGCEGPGMPQPLPSFSVEEFFEFDGPSAAPWAFLGPAQQLRADASGGSRGCCQIDASRLRDDRSEDGAGSRSSVLGERQIFARCPGPLHTLGAAPPRQRSSQRQGESNTTPVTVGRRRARLESTESVDGSLERSLRTTVELNNVEENEEVIHLEELNRPVEAAHKPRRRFALRYGHQHSPGTVVATEKFLNAALVRNALGTLNADLPDPVPTPGLGRLNSQFNPAETGRLLRCAVSEGMKDCEPKPRAAGEDAVKPRKKRRRRVAFLQRGSSACFAFEFHAPTGSEAEFRQLGVDAGLEPADRISALMRMGEIESDHRACTSPECSFGPVCGQTAFNAWGDSVRFKSLRIPSSAFRVARAFRQSGKQRGYRLGRDTLDDSFEVEECPSGGCAGCTTVGNLHEWAEGYPLGEPSDEAANKRLLMDEPSLMDPPRCNPLRDRRQRSACRREGVDLPVFSASVAWISLRQPQSHSLAPSDNQEQHEPYPSSDTRRDPSGTAVPADCGGGQGGCARGEPPLHQRANTHEVPGQALNGPALPLRASPSFAFSLAAPNTPLRGMAPGVDEPDGLSRQEQVATAMTAPDSSEAGLSIVDSLFRFQRSFFRSWGPENTINSGLTSRVRCLHFGSDFHNESGARAPRLAACDVSFSGDLFLISQTTDELHDAGSSPALAAPPRPRPNRPDAALYGPPTFFDAAVAADQGHEDIKSHVTSGDNTHLCRSLFRRRGTMELRLNARAAGAREVEGKGGRSPRAHPLRTLRVELPYSPRLRSPQSGSSTFQEPGNISDRRDVPPRISQGAQDGRDARVQPLLPEQPSNSEEMFGVPGQSEALRPQSALLAAMSPEERALVPVNPNGSNLPDAFTPPPISILLDPPAGGGEYEEIRCFEAFGRECFGASERVTRTLPGSMIAPILTSPFPEPGSNEHTPPVSAPQSAELAEEDSESAVTFTKAQEFTEKQEWAFRFDTEANPFLSLLPLDGQLDAGAGRNALGRAIVRLREAVELSCFSKRRTVYTGPETGAERASMLVRDRNRFPIPVEGGWSEELAITGETCMTSLAVDRKIRICPATARMVVREAGSAARSVPVLAIDVHDAAFPASSEVRKSYAPIAQRDEYKRRVHIRSRKASSSETPQARAPHDGPLSVSVAAYGAGRLGSAQVFLSAALIQRVFHGERASDQRPVGGNLESSTPACSSVQPSTFTRATEFLVEVYAEACQGRVWRRRCSCRPVLQRYDCETVLTDPRELREEPALSAEPASSCPPDAAILQRGISTTLNDRISGERIRCEGPNELLAPIFDNVVAEGGSASGPGKGAVSTSSPVAGPSQAMAQVPSAFTVVFNHSAPLVLQCNSLNGFLRRTAWTKRDDTMSLFSLRNPPRVFAEPDEPAIEERPEQSPGNAPQGSRAMNRDTRRRSEVRLGEFPRTYWGSQYRLAPTETGSGATLTGTRNQGYSVAGMATFRSGTVAVSIERCSNGLERLHVCGVLGTSKDDPPADQGPAIGYARGLEMASGTLQRADFAAPNGSDVLEGMGGAPGTAQPGHEELWLERPREALFCRQRVPDPVYHRTWPIIGCNPPIPSLPCNSLFEALSAIITSHSLSDPESAPYSEVPSEEPPVPDAPADPWAWVARPRAREGAKDRSRVYNGALLSSEEESTRDSTQGCALTGPEIPLECLKREMRHKSHHVNAVHSLDKTPQVRLAQLAQSSSKFFRPSSDLRQLSTCEQHYGESALPDDAAPLVGRRDRGMEKDAALHTGSGDSQVRPCTTGARTPPCEGASPSTLCLNSCSEIYHVAKRLETRAEKELIDALAGRQEMAESSVRRHEQENSLERPIPHGTETPSPFEHRSTPGLPENTPERERFASEEAQSVAANMSAPAPAFDDREPVPPVPRTQSRRLESDPAPVATPPGVNQRLACRDRTENDNFAQRSSSFGSVHDISSVGPTETTRRVLYGLPGLGYTLLSGPGGNGNDLQSAAEFPDGTLLTARLRHLRRRTRIARGSPLLGSTATGPWQGSLFTLRRERRSTGLSLGERQAWYQVARRRVDATQELDYLHVVSSGPAEALALFEEESADAPLRVARVGWILARRESYVSRVFGWIPLHKCVAGSLCSLDDRQLAANGNRYSIQPSEIQASPVSFERVCRAEIRACEVAEQAESVGLNEPRFSLVRNAFSRGLAESGERSSLKSSPGLVPDSHSSPGGPRAFSATQNSVRNEQAAGLTLPHVGGSPLVVSTVPINFATGGSDAVSNSSRERHSRAESQLDKRDEPKSGSKRPQPCHALIRSVCVIRNETDESGNLTLCGFDRVSPLTRSSHDQCPPQSGPQQVNPPPWARFQCLVQLIGLTSAFDEESPCPRRSLLVFDLLCHTSRRSRSAAVVTSPQVPSLPTSTIPVHEETVYFAGEDDSGADKLPPRGARGGESIGRRDAAESAESHPSELGRYGAQPAVLLAVPVAPAPPVTVRATTSEDAYFRSIPPADDEPPAARSSPEPEAVRAPVPPQCTPRLVCGLVHQATSPGVFQNGGTEPLWDQLPRVGSAAELSGRGHESCDGARPVNGLHRIGDTTSPHLKADEYAAAGLEVGDELSWMEVVYESTGFDIEPVESLFRVCSDEDVRRIRASQGAAANVPLGEHGMRDANLAIDRAAVCRAGTFLSPYAEIRQLPGQEFERGFALLDLGMRRGGEQERSTLTAPDRSWLEAEAEPMRSALPGAATVLESEWGAEGRSLRGRRVRQAPERPESSRGREPHHAKTACFRRDYEASPLPSSDSGRAEHGYRITHRHQYGQAPPRSAEASHVEGSLLALVTDEDEWVPRRAALVADAGGRRRARRDESLRELEQLRRGGFRAGNSLVADERSKTAPTCDRFSSRSEKLECQEFFSPMFARSRTESLEVQCAVDQEVSASEDVQSVPPGFAALFALPVEFASTQNSSCAAPNEYLERYCATDRLVRASKRLGLDHGATPRNWCRAAARSTLPEVERSLKPFVALHLSYGKGVEGFWANLGKGESIGDRAVGHDPLFKVSPEDGLDSGARCAGPGPQPRDGVEGLVPAMSIADTLDEKSLGSPLPLRHLRVARHLFGSPLFVEDVQNTPRDLREIWYAKFRDRGRPARVFSRDLRETAIARRLVKFEGRLSRAIKESSDNAYDETLPSPNDGPGETVVAMCDGATQAEGSQRRGTRRPAIFFACNQTPTARLFERRETEQHRWSVLKRLSALGRCDAGPQYRVSNTSLNFSACERKVWLEKKGGWKSRRGGILFTRLNRQVTGFEETTNLQPPPSDSQEPRPVPAAVPSPLVDHAVGTRSFPRLEPFCSAEGTRFSNATDSGAQGEERLNAIKPNCGTPACRDLGGGVEVASREVTAPQPALRPQESLSARRRSSWSLTPISHPSPVVSPLISSRGPSFEAALRSLSTEVAFTDEPTHDNERRRELRELGAAPSGRVPRDEHLRKFPGQGARMLRESSSQFSRARRSLAVNESTASFEEPGTFDVTTTAAAQCAVADFTSPSAHDPRRGDLDQIPAGSLSLPSSCTCGDSATGLGQAIVPPAITSRLPCRGLLVSELLRIRLASQGLGRGTCTSIRTCTERAWSRGAWPEMDSEMIQESTSETAGANTENLGIVAHLGAQQELTARVRRRRRLPVAHGLDLAFNRGEGKEPNQQLIPTLPELLVSARAGIRGIRTQFSPMAGGASSRNVVMMIVKGQTTSVYAAERSLTLCRRLDLRLSSKETHHAAYSRVHRAPFQAGIGSAELACLLANPAFEPGVLTFSVIQSVTGTEASWRYQGRDQPLSPPIHSRPPARAGPLDSEAAVAAQLSLNIEVARSEAPTSINGSMAAAAPLGLSSRGTSSESEPAGPPMNLPCMSMEPPADVLEGALAVGPFTGPREERLPCSEADPLFLRSLEANVETGAGRSSYSSAQERSIEDWVEAPTAYAPLEDEPSAASCSARHRTSHTSPQTLPQRTGCSRKRATFKSVKSGSRTDRLRSPSVNLGRTTGTRTDSFLNPIPESWQTAMSADVDKSEVSFRTPKMSPSQRPEPPSLDPTEQSAGAPALFMSSHAAIRQLGVSDAPRPSRRKPGGTSHYAELRVPPGTASRSPSAESGQLQVPDRSSIVLESQDYEQDSPLTPGMVNAYQPISFPESAGAPPGLLAAPDTPVDGNRPVVVFGLPQTLIRDIPDSGLAGLVPQAPAASLYAYYGQIARQFKTSSRRLGLRIRQERCWTQRLRRARQSNYAASGIAGAAFIRSRRRAHETGRTAHNASESTAFTENAACSRRRRMPLDGGPYESHLRQEGASTEAPLLGDPLHSDAGGAPPRIRVSGLWSQPRQDHEPYGCLLTSGTLVSLFPQARCERLAFATMAANLHDPIPISHPDAANTLDLPLLYEDLLGAGFGRENRDGAGANACSASTSAVGPRQGGPTIRLAGGPVTCRQRLLISQWSPHAESPPGVMPEQLGALLLYGMTRAQSFYDITSFLALDVELFEPLVPPESDSVNSFFGAILVVRLAQAVVHTADNSLCLSLLTFADRDVNKRSGTGDRRKRARLMRDVDVRTTIFRARQERAPLAQAPEFGELLAQGRCEEQADDSLIFIAERSRAWEPECTRAGPRRERCRSGHVSGNYRVVELEGPSAGLAGLALVVESDVVFNQRPADPLLYPGRGGAERVGLNNARGCSLQSEAEARVLVRLLCLAGINRARIPWPRETQLVEPPQEQWGANPLEFLPYYLVPSAVTLQVSLLSDGDRWGAARQLARRENVYRLEARDDPPQLASLRIDDECRLRFQMDQAGVWSVSAPAMPSVPPPEPALDDSRELGSGNLEPSAFTRLESCMRDSGQLACGVAQRANRHGLPVILMTQPEAIATACAIARSQRFFKLPAVHFRSRSLADSRRVPPLSGRIRGDYERGFRDVDDSTEEHERIQMGGVTTRTGVQSAPMLTRSRPPSAGTASREVPECGAGAPVMAAQPTTCFERLMYLARGKLEVQEMLVKAALLPNLKGFEYRAVESMRFSHDREELERSPWAAQAARDPARPRLTGEMSESQDPTVPLLRLPGESLGCPEFCEISGQLRALASLAPRHLLAHTNGGVMLRTDNPQEFEGILVGRAEEDDLAARQNGSQVTHALNSLPDPLAAFGATDLALWDHRGEYRAELQVGPQAMALYDDIGAVQAPDETSPDCRHAATASGGPLTAGMAVNAPMALRAPNQARHAKFLDSAADKTNVSTYVLKAANRLRLAEYEIREWTQSQSGLPAELVGVVMASAALDVKSGSYMPVERSVTSAYRYFEWSSPRARTALQADINDANPEHQTICPENAALPALYTLTESVLEAIRLCLSRAGGIAEWASRHDASYARAGGMVVASSGDVELPQYSGAPSLGLDARGQPSQAPAPSQPDEPELLQTIPMSAAELFSYSAEASIGSFSQGPGEFEDQASGGRRRDSPTNLSDVDVTASREAGYLPERRLRLRDRELLRHTGAILARETRGLERTGGLTVGLSQNSESNLRSLSVANVGSCPMGGAIFPIHHKLSTAGSPQESLLASMEGETEKGVKSEFCQLAILTRRRFDPEAGARFKRAMGSTQNDCEIESNAGSNRIDGGRAKDTGFLHAELMEDAADLYVRGSESLSALERGPDDLFELFEECSLSEALKMEAELGAGEALSQFEAEDLPTPVECEQSVSVLERFLMHGHTAQEVAGLSRVVKSTVCDSAYRIREQSFEEHEAHDEAVKKFKNDAQRAHTFRIRCPRVADYLVPYEAPSKEQSAVIRTHQADALVHEDSRTALGWLASIYXGRSPSVGSDVSDSKFPKFAMKNSTRKKLKGDDSAITSAYVASAGGSSMGILSG</Seq>
  <cvParam accession="MS:1001088" name="protein description" cvRef="PSI-MS"
    value="Rnd2psu|NC_LIV_080090 Decoy sequence, was | organism=Neospora_caninum | product=hypothetical protein | location=Neo_chrVIIa:229175-282694(-) | length=16207"
  />
</DBSequence>

<cvParam accession="MS:1001088" cvRef="PSI-MS" value="Rnd3psu|NC_LIV_083320 Rnd3psu|NC_LIV_083320 Decoy sequence, was | organism=Neospora_caninum | product=zinc finger (CCCH type) protein, putative | location=Neo_chrVIIa:3989308-3992771(+) | length=661" name="protein description"/>

<DataCollection>
<Inputs xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
    <SourceFile location="build/classes/resources/55merge_omssa.omx" id="SourceFile_1">
        <FileFormat>
            <cvParam accession="MS:1001400" cvRef="PSI-MS" name="OMSSA xml file"/>
        </FileFormat>
    </SourceFile>
  ...
</DataCollection>

<DatabaseFilters>
  <Filter>
    <FilterType>
      <cvParam accession="MS:1001020" name="DB filter taxonomy" cvRef="PSI-MS"/>
    </FilterType>
  </Filter>
</DatabaseFilters>

<DatabaseName>
    <userParam name="D:/Software/Databases/Neospora_3rndTryp/Neo_rndTryp_3times.fasta"/>
</DatabaseName>

Path /MzIdentML/DataCollection/Inputs/SearchDatabase/DatabaseName
MAY supply a *child* term of MS:1001013 (database name) one or more times
  e.g.: MS:1001084 (database nr) 
  e.g.: MS:1001104 (database SwissProt) 
  e.g.: MS:1001142 (database IPI_human) 
  e.g.: MS:1001285 (database IPI_mouse) 
  e.g.: MS:1001286 (database IPI_rat) 
  e.g.: MS:1001287 (database IPI_zebrafish) 
  e.g.: MS:1001288 (database IPI_chicken) 
  e.g.: MS:1001289 (database IPI_cow) 
  e.g.: MS:1001290 (database IPI_arabidopsis) 

<cvParam accession="MS:1001073" name="database type amino acid" cvRef="PSI-MS"/>

<userParam name="Neo_rndTryp_3times.fasta"/>
<userParam name="D:/Software/Databases/Neospora_3rndTryp/Neo_rndTryp_3times.fasta"/>

<Enzyme id="ENZ_0" cTermGain="OH" nTermGain="H" semiSpecific="0">
  <SiteRegexp><![CDATA[(?<=[KR])(?!P)]]></SiteRegexp>
  <EnzymeName>
    <cvParam accession="MS:1001251" name="Trypsin" cvRef="PSI-MS"/>
  </EnzymeName>
</Enzyme>

<EnzymeName>
    <cvParam accession="MS:1001251" cvRef="PSI-MS" name="Trypsin"/>
</EnzymeName>

Path /MzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/Enzymes/Enzyme/EnzymeName
MAY supply a *child* term of MS:1001045 (cleavage agent name) only once
  e.g.: MS:1001091 (NoEnzyme) 
  e.g.: MS:1001251 (Trypsin) 
  e.g.: MS:1001303 (Arg-C) 
  e.g.: MS:1001304 (Asp-N) 
  e.g.: MS:1001305 (Asp-N_ambic) 
  e.g.: MS:1001306 (Chymotrypsin) 
  e.g.: MS:1001307 (CNBr) 
  e.g.: MS:1001308 (Formic_acid) 
  e.g.: MS:1001309 (Lys-C) 
  e.g.: MS:1001310 (Lys-C/P) 
  et al.

<cvParam accession="MS:1001251" name="Trypsin" cvRef="PSI-MS"/>

<Enzymes>
  <Enzyme id="ENZ_0" cTermGain="OH" nTermGain="H" semiSpecific="0">
    <SiteRegexp><![CDATA[(?<=[KR])(?!P)]]></SiteRegexp>
    <EnzymeName>
      <cvParam accession="MS:1001251" name="Trypsin" cvRef="PSI-MS"/>
    </EnzymeName>
  </Enzyme>
  ...
</Enzymes>

Path /MzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/DatabaseFilters/Filter/Exclude
MAY supply a *child* term of MS:1001512 (Sequence database filters) one or more times
  e.g.: MS:1001090 (taxonomy nomenclature) 
  e.g.: MS:1001201 (DB MW filter maximum) 
  e.g.: MS:1001202 (DB MW filter minimum) 
  e.g.: MS:1001203 (DB PI filter maximum) 
  e.g.: MS:1001204 (DB PI filter minimum) 
  e.g.: MS:1001467 (taxonomy: NCBI TaxID) 
  e.g.: MS:1001468 (taxonomy: common name) 
  e.g.: MS:1001469 (taxonomy: scientific name) 
  e.g.: MS:1001470 (taxonomy: Swiss-Prot ID) 
  e.g.: MS:1001513 (DB sequence filter pattern) 
  et al.

<FileFormat>
    <cvParam accession="MS:1001062" cvRef="PSI-MS" name="Mascot MGF file"/>
</FileFormat>

Path /MzIdentML/DataCollection/Inputs/SearchDatabase/FileFormat
MUST supply a *child* term of MS:1001347 (database file formats) one or more times
  e.g.: MS:1001348 (FASTA format) 
  e.g.: MS:1001349 (ASN.1) 
  e.g.: MS:1001350 (NCBI *.p*) 
  e.g.: MS:1001351 (clustal aln) 
  e.g.: MS:1001352 (embl em) 
  e.g.: MS:1001353 (NBRF PIR) 
  e.g.: MS:1001462 (PEFF format) 

Path /MzIdentML/DataCollection/Inputs/SourceFile/FileFormat
MUST supply a *child* term of MS:1001040 (intermediate analysis format) only once
  e.g.: MS:1000742 (Bioworks SRF file) 
  e.g.: MS:1001107 (data stored in database) 
  e.g.: MS:1001199 (Mascot DAT file) 
  e.g.: MS:1001200 (Sequest out file) 
  e.g.: MS:1001242 (Sequest out folder) 
  e.g.: MS:1001243 (Sequest summary) 
  e.g.: MS:1001275 (ProteinScape SearchEvent) 
  e.g.: MS:1001276 (ProteinScape Gel) 
  e.g.: MS:1001399 (OMSSA csv file) 
  e.g.: MS:1001400 (OMSSA xml file) 
  et al.

Path /MzIdentML/DataCollection/Inputs/SpectraData/FileFormat
MUST supply a *child* term of MS:1000560 (mass spectrometer file format) one or more times
  e.g.: MS:1000526 (Waters raw file) 
  e.g.: MS:1000562 (ABI WIFF file) 
  e.g.: MS:1000563 (Thermo RAW file) 
  e.g.: MS:1000564 (PSI mzData file) 
  e.g.: MS:1000565 (Micromass PKL file) 
  e.g.: MS:1000566 (ISB mzXML file) 
  e.g.: MS:1000567 (Bruker/Agilent YEP file) 
  e.g.: MS:1000584 (mzML file) 
  e.g.: MS:1000613 (DTA file) 
  e.g.: MS:1000614 (ProteinLynx Global Server mass spectrum XML file) 
  et al.

<cvParam accession="MS:1001199" name="Mascot DAT file" cvRef="PSI-MS"/>
<cvParam accession="MS:1001348" name="FASTA format" cvRef="PSI-MS"/>
<cvParam accession="MS:1001062" name="Mascot MGF file" cvRef="PSI-MS"/>
<cvParam accession="MS:1001400" cvRef="PSI-MS" name="OMSSA xml file"/>

<Filter>
  <FilterType>
    <cvParam accession="MS:1001020" name="DB filter taxonomy" cvRef="PSI-MS"/>
  </FilterType>
</Filter>

<FilterType>
  <cvParam accession="MS:1001020" name="DB filter taxonomy" cvRef="PSI-MS"/>
</FilterType>

Path /MzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/DatabaseFilters/Filter/FilterType
MUST supply a *child* term of MS:1001511 (Sequence database filter types) one or more times
  e.g.: MS:1001020 (DB filter taxonomy) 
  e.g.: MS:1001021 (DB filter on accession numbers) 
  e.g.: MS:1001022 (DB MW filter) 
  e.g.: MS:1001023 (DB PI filter) 
  e.g.: MS:1001027 (DB filter on sequence pattern) 

<cvParam accession="MS:1001020" name="DB filter taxonomy" cvRef="PSI-MS"/>

<FragmentTolerance>
  <cvParam accession="MS:1001412" name="search tolerance plus value" value="0.8"
    cvRef="PSI-MS" unitAccession="UO:0000221" unitName="dalton" unitCvRef="UO"/>
  <cvParam accession="MS:1001413" name="search tolerance minus value" value="0.8"
    cvRef="PSI-MS" unitAccession="UO:0000221" unitName="dalton" unitCvRef="UO"/>
</FragmentTolerance>

Path /MzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/FragmentTolerance
MUST supply term MS:1001412 (search tolerance plus value) only once
MUST supply term MS:1001413 (search tolerance minus value) only once

<cvParam accession="MS:1001412" name="search tolerance plus value" value="0.8"
<cvParam accession="MS:1001413" name="search tolerance minus value" value="0.8"

<FragmentationTable>
    <Measure id="Measure_MZ">
        <cvParam accession="MS:1001225" cvRef="PSI-MS" unitCvRef="PSI-MS" unitName="m/z" unitAccession="MS:1000040" name="product ion m/z"/>
    </Measure>
    <Measure id="Measure_Int">
        <cvParam accession="MS:1001226" cvRef="PSI-MS" name="product ion intensity"/>
    </Measure>
  ...
</FragmentationTable>

Path /MzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/DatabaseFilters/Filter/Include
MAY supply a *child* term of MS:1001512 (Sequence database filters) one or more times
  e.g.: MS:1001090 (taxonomy nomenclature) 
  e.g.: MS:1001201 (DB MW filter maximum) 
  e.g.: MS:1001202 (DB MW filter minimum) 
  e.g.: MS:1001203 (DB PI filter maximum) 
  e.g.: MS:1001204 (DB PI filter minimum) 
  e.g.: MS:1001467 (taxonomy: NCBI TaxID) 
  e.g.: MS:1001468 (taxonomy: common name) 
  e.g.: MS:1001469 (taxonomy: scientific name) 
  e.g.: MS:1001470 (taxonomy: Swiss-Prot ID) 
  e.g.: MS:1001513 (DB sequence filter pattern) 
  et al.

<InputSpectra spectraData_ref="SID_1"/>

<InputSpectrumIdentifications spectrumIdentificationList_ref="SIL_1"/>

<Inputs xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
    <SourceFile location="build/classes/resources/55merge_omssa.omx" id="SourceFile_1">
        <FileFormat>
            <cvParam accession="MS:1001400" cvRef="PSI-MS" name="OMSSA xml file"/>
        </FileFormat>
    </SourceFile>
    <SearchDatabase numDatabaseSequences="22348" location="D:/Software/Databases/Neospora_3rndTryp/Neo_rndTryp_3times.fasta" id="SearchDB_1">
  ...
</Inputs>

Path /MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/SpectrumIdentificationResult/SpectrumIdentificationItem/Fragmentation/IonType
MAY supply a *child* term of MS:1001221 (fragmentation information) one or more times
  e.g.: MS:1000903 (product ion series ordinal) 
  e.g.: MS:1000904 (product ion m/z delta) 
  e.g.: MS:1000926 (product interpretation rank) 
  e.g.: MS:1001220 (frag: y ion) 
  e.g.: MS:1001222 (frag: b ion - H2O) 
  e.g.: MS:1001223 (frag: y ion - H2O) 
  e.g.: MS:1001224 (frag: b ion) 
  e.g.: MS:1001225 (product ion m/z) 
  e.g.: MS:1001226 (product ion intensity) 
  e.g.: MS:1001227 (product ion m/z error) 
  et al.

<MassTable id="MT" msLevel="1 2">
  <Residue code="A" mass="71.037114"/>
  <Residue code="C" mass="103.009185"/>
  <Residue code="D" mass="115.026943"/>
  <Residue code="E" mass="129.042593"/>
  <Residue code="F" mass="147.068414"/>
  <Residue code="G" mass="57.021464"/>
  ...
</MassTable>

Path /MzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/MassTable
MAY supply a *child* term of MS:1001354 (mass table options) one or more times
  e.g.: MS:1001346 (AAIndex mass table) 

<Measure id="Measure_Error">
    <cvParam accession="MS:1001227" cvRef="PSI-MS" unitCvRef="PSI-MS" unitName="m/z" unitAccession="MS:1000040" name="product ion m/z error"/>
</Measure>

Path /MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/FragmentationTable/Measure
MUST supply term MS:1001226 (product ion intensity) only once
MUST supply term MS:1001225 (product ion m/z) only once
MUST supply term MS:1001227 (product ion m/z error) only once

<cvParam cvRef="PSI-MS" accession="MS:1001225" name="product ion m/z"/>
<cvParam cvRef="PSI-MS" accession="MS:1001226" name="product ion intensity"/>
<cvParam cvRef="PSI-MS" accession="MS:1001227" name="product ion m/z error"

<Modification location="11" residues="M" monoisotopicMassDelta="15.994915">
  <cvParam accession="UNIMOD:35" name="Oxidation" cvRef="UNIMOD"/>
  <cvParam accession="MS:1001524" name="fragment neutral loss" cvRef="PSI-MS"
    value="63.998285" unitAccession="UO:0000221" unitName="dalton" unitCvRef="UO"/>
</Modification>

<cvParam accession="UNIMOD:4" name="Carbamidomethyl" cvRef="UNIMOD"/>
<cvParam accession="UNIMOD:35" name="Oxidation" cvRef="UNIMOD"/>
<cvParam accession="MS:1001524" name="fragment neutral loss" cvRef="PSI-MS" value="0"

<ModificationParams>
    <SearchModification residues="C" massDelta="57.021465" fixedMod="true">
        <cvParam accession="UNIMOD:4" cvRef="UNIMOD" name="Carbamidomethyl"/>
    </SearchModification>
    <SearchModification residues="M" massDelta="15.994915" fixedMod="false">
        <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
    </SearchModification>
  ...
</ModificationParams>

<Organization id="ORG_MSL" name="Matrix Science Limited"/>

<ParentTolerance>
  <cvParam accession="MS:1001412" name="search tolerance plus value" value="1.5"
    cvRef="PSI-MS" unitAccession="UO:0000221" unitName="dalton" unitCvRef="UO"/>
  <cvParam accession="MS:1001413" name="search tolerance minus value" value="1.5"
    cvRef="PSI-MS" unitAccession="UO:0000221" unitName="dalton" unitCvRef="UO"/>
</ParentTolerance>

Path /MzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ParentTolerance
MUST supply term MS:1001412 (search tolerance plus value) only once
MUST supply term MS:1001413 (search tolerance minus value) only once

<cvParam accession="MS:1001412" name="search tolerance plus value" value="1.5"
<cvParam accession="MS:1001413" name="search tolerance minus value" value="1.5"

<Peptide id="TVDVGMGGVDLANLKACSGSGVSQELHIWGK_000000100000000000000000000000000">
  <PeptideSequence>TVDVGMGGVDLANLKACSGSGVSQELHIWGK</PeptideSequence>
  <Modification location="6" residues="M" monoisotopicMassDelta="15.994915">
    <cvParam accession="UNIMOD:35" name="Oxidation" cvRef="UNIMOD"/>
    <cvParam accession="MS:1001524" name="fragment neutral loss" cvRef="PSI-MS"
      value="63.998285" unitAccession="UO:0000221" unitName="dalton" unitCvRef="UO"/>
  </Modification>
  ...
</Peptide>

<PeptideEvidence id="DDDHSDQGGEVQGGR_00000000000000000_1_Rnd2psu|NC_LIV_123110_2144_2158"
  start="2144" end="2158" pre="R" post="G" isDecoy="false"
  dBSequence_ref="DBSeq_1_Rnd2psu|NC_LIV_123110" peptide_ref="DDDHSDQGGEVQGGR_00000000000000000"/>
<PeptideEvidence id="SVAGKGLADEHTACR_00000000000000000_1_Rnd3psu|NC_LIV_114310_1396_1410"
  start="1396" end="1410" pre="R" post="E" isDecoy="false"
  dBSequence_ref="DBSeq_1_Rnd3psu|NC_LIV_114310" peptide_ref="SVAGKGLADEHTACR_00000000000000000"/>
<PeptideEvidence id="FASCCGEDDGEAPR_0000000000000000_1_psu|NC_LIV_113540_2484_2497" start="2484"
  ...
</PeptideEvidence>

<PeptideEvidenceRef
  peptideEvidence_ref="SGALR_0000000_1_Rnd1psu|NC_LIV_081600_1089_1093"/>
<PeptideEvidenceRef peptideEvidence_ref="SGALR_0000000_1_Rnd1psu|NC_LIV_020100_977_981"/>
<PeptideEvidenceRef peptideEvidence_ref="SGALR_0000000_1_Rnd1psu|NC_LIV_102910_725_729"/>
<PeptideEvidenceRef peptideEvidence_ref="SGALR_0000000_1_Rnd1psu|NC_LIV_122850_402_406"/>
<PeptideEvidenceRef peptideEvidence_ref="SGALR_0000000_1_Rnd1psu|NC_LIV_060960_32_36"/>
<PeptideEvidenceRef peptideEvidence_ref="SGALR_0000000_1_Rnd2psu|NC_LIV_145280_820_824"/>
  ...
</PeptideEvidenceRef>

<cvParam accession="MS:1001171" name="mascot:score" cvRef="PSI-MS" value="13.49"/>
<cvParam accession="MS:1001172" name="mascot:expectation value" cvRef="PSI-MS"
<cvParam accession="MS:1001363" name="peptide unique to one protein" cvRef="PSI-MS"/>
<cvParam accession="MS:1001371" name="mascot:identity threshold" cvRef="PSI-MS" value="42"/>
<cvParam accession="MS:1001370" name="mascot:homology threshold" cvRef="PSI-MS" value="24"/>
<cvParam accession="MS:1001030" name="number of peptide seqs compared to each spectrum"
<cvParam accession="MS:1000796" name="spectrum title" cvRef="PSI-MS"

<PeptideHypothesis
  peptideEvidence_ref="KDLYGNVVLSGGTTMYEGIGER_000000000000000100000000_1_psu|NC_LIV_020800_292_313">
  <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_303_1"/>
  <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_304_1"/>
</PeptideHypothesis>

<cvParam accession="MS:1001171" name="mascot:score" cvRef="PSI-MS"
<cvParam accession="MS:1001093" name="sequence coverage" cvRef="PSI-MS" value="11"/>
<cvParam accession="MS:1001097" name="distinct peptide sequences" cvRef="PSI-MS"

<PeptideSequence>GELLGLGGVSGCPLRSGGTEAGGALEQPPLKPK</PeptideSequence>

<Person firstName="firstname" lastName="secondName" id="PERSON_DOC_OWNER">
    <Affiliation organization_ref="ORG_DOC_OWNER"/>
</Person>

<ProteinAmbiguityGroup id="PAG_hit_2">
  <ProteinDetectionHypothesis id="PDH_psu|NC_LIV_105380_0"
    dBSequence_ref="DBSeq_1_psu|NC_LIV_105380" passThreshold="true">
    <PeptideHypothesis
      peptideEvidence_ref="VIDENFGLVEGLMTTVHAATGTQK_00000000000001000000000000_1_psu|NC_LIV_105380_842_865">
      <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_307_1"/>
    </PeptideHypothesis>
  ...
</ProteinAmbiguityGroup>

<ProteinDetection id="PD_1" proteinDetectionProtocol_ref="PDP_MascotParser_1"
  proteinDetectionList_ref="PDL_1" activityDate="2011-03-25T13:33:51">
  <InputSpectrumIdentifications spectrumIdentificationList_ref="SIL_1"/>
</ProteinDetection>

<ProteinDetectionHypothesis id="PDH_psu|NC_LIV_105380_0"
  dBSequence_ref="DBSeq_1_psu|NC_LIV_105380" passThreshold="true">
  <PeptideHypothesis
    peptideEvidence_ref="VIDENFGLVEGLMTTVHAATGTQK_00000000000001000000000000_1_psu|NC_LIV_105380_842_865">
    <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_307_1"/>
  </PeptideHypothesis>
  <cvParam accession="MS:1001171" name="mascot:score" cvRef="PSI-MS" value="99.72"/>
  ...
</ProteinDetectionHypothesis>

Path /MzIdentML/DataCollection/AnalysisData/ProteinDetectionList/ProteinAmbiguityGroup/ProteinDetectionHypothesis
MAY supply a *child* term of MS:1001153 (search engine specific score) one or more times
  e.g.: MS:1001154 (Sequest:probability) 
  e.g.: MS:1001155 (Sequest:xcorr) 
  e.g.: MS:1001156 (Sequest:deltacn) 
  e.g.: MS:1001157 (Sequest:sp) 
  e.g.: MS:1001158 (Sequest:Uniq) 
  e.g.: MS:1001159 (Sequest:expectation value) 
  e.g.: MS:1001160 (Sequest:sf) 
  e.g.: MS:1001161 (Sequest:matched ions) 
  e.g.: MS:1001162 (Sequest:total ions) 
  e.g.: MS:1001163 (Sequest:consensus score) 
  et al.
MAY supply a *child* term of MS:1001060 (quality estimation method details) one or more times
  e.g.: MS:1001058 (quality estimation by manual validation) 
  e.g.: MS:1001194 (quality estimation with decoy database) 
  e.g.: MS:1001447 (prot:FDR threshold) 
  e.g.: MS:1001448 (pep:FDR threshold) 
  e.g.: MS:1001454 (quality estimation with implicite decoy sequences) 
  e.g.: MS:1001494 (no threshold) 
  e.g.: MS:1001574 (report only spectra assigned to identified proteins) 
MAY supply a *child* term of MS:1001085 (protein result details) one or more times
  e.g.: MS:1001088 (protein description) 
  e.g.: MS:1001090 (taxonomy nomenclature) 
  e.g.: MS:1001093 (sequence coverage) 
  e.g.: MS:1001097 (distinct peptide sequences) 
  e.g.: MS:1001098 (confident distinct peptide sequences) 
  e.g.: MS:1001099 (confident peptide qualification) 
  e.g.: MS:1001100 (confident peptide) 
  e.g.: MS:1001125 (manual validation) 
  e.g.: MS:1001157 (Sequest:sp) 
  e.g.: MS:1001158 (Sequest:Uniq) 
  et al.

<ProteinDetectionList id="PDL_1">
  <ProteinAmbiguityGroup id="PAG_hit_1">
    <ProteinDetectionHypothesis id="PDH_psu|NC_LIV_020800_0"
      dBSequence_ref="DBSeq_1_psu|NC_LIV_020800" passThreshold="true">
      <PeptideHypothesis
        peptideEvidence_ref="LCYIALDFDEEMKAAEDSSDIEK_0000000000001000000000000_1_psu|NC_LIV_020800_217_239">
        <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_308_1"/>
  ...
</ProteinDetectionList>

Path /MzIdentML/DataCollection/AnalysisData/ProteinDetectionList
MAY supply a *child* term of MS:1001184 (search statistics) one or more times
  e.g.: MS:1001035 (date / time search performed) 
  e.g.: MS:1001036 (search time taken) 
  e.g.: MS:1001177 (number of molecular hypothesis considered) 

<ProteinDetectionProtocol id="PDP_MascotParser_1" analysisSoftware_ref="AS_mascot_parser">
  <AnalysisParams>
    <cvParam accession="MS:1001316" name="mascot:SigThreshold" cvRef="PSI-MS" value="0.05"/>
    <cvParam accession="MS:1001317" name="mascot:MaxProteinHits" cvRef="PSI-MS" value="Auto"/>
    <cvParam accession="MS:1001318" name="mascot:ProteinScoringMethod" cvRef="PSI-MS"
      value="MudPIT"/>
    <cvParam accession="MS:1001319" name="mascot:MinMSMSThreshold" cvRef="PSI-MS" value="0"/>
  ...
</ProteinDetectionProtocol>

<Provider id="PROVIDER">
  <ContactRole contact_ref="PERSON_DOC_OWNER">
    <Role>
      <cvParam accession="MS:1001271" name="researcher" cvRef="PSI-MS"/>
    </Role>
  </ContactRole>
</Provider>

<Residue code="C" mass="103.009185"/>

<Role>
  <cvParam accession="MS:1001267" name="software vendor" cvRef="PSI-MS"/>
</Role>

<cvParam accession="MS:1001267" name="software vendor" cvRef="PSI-MS"/>
<cvParam accession="MS:1001271" name="researcher" cvRef="PSI-MS"/>

<SearchDatabase numDatabaseSequences="22348" location="D:/Software/Databases/Neospora_3rndTryp/Neo_rndTryp_3times.fasta" id="SearchDB_1">
    <FileFormat>
        <cvParam accession="MS:1001348" cvRef="PSI-MS" name="FASTA format"/>
    </FileFormat>
    <DatabaseName>
        <userParam name="D:/Software/Databases/Neospora_3rndTryp/Neo_rndTryp_3times.fasta"/>
    </DatabaseName>
  ...
</SearchDatabase>

Path /MzIdentML/DataCollection/Inputs/SearchDatabase
MAY supply a *child* term of MS:1000561 (data file checksum type) one or more times
  e.g.: MS:1000568 (MD5) 
  e.g.: MS:1000569 (SHA-1) 
MAY supply a *child* term of MS:1001011 (search database details) one or more times
  e.g.: MS:1001014 (database local file path) 
  e.g.: MS:1001015 (database original uri) 
  e.g.: MS:1001016 (database version) 
  e.g.: MS:1001017 (database release date) 
  e.g.: MS:1001020 (DB filter taxonomy) 
  e.g.: MS:1001021 (DB filter on accession numbers) 
  e.g.: MS:1001022 (DB MW filter) 
  e.g.: MS:1001023 (DB PI filter) 
  e.g.: MS:1001024 (translation frame) 
  e.g.: MS:1001025 (translation table) 
  et al.

<SearchDatabaseRef searchDatabase_ref="SDB_NeoProt_tripledecoy"/>

<SearchModification residues="C" massDelta="57.021465" fixedMod="true">
    <cvParam accession="UNIMOD:4" cvRef="UNIMOD" name="Carbamidomethyl"/>
</SearchModification>

Path /MzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ModificationParams/SearchModification
MUST supply a *child* term of UNIMOD:0 (UNIMOD root) one or more times
MUST supply a *child* term of MS:1001471 (peptide modification details) one or more times
  e.g.: MS:1001460 (unknown modification) 
  e.g.: MS:1001524 (fragment neutral loss) 
  e.g.: MS:1001525 (precursor neutral loss) 
MUST supply a *child* term of MOD:00000 (protein modification) one or more times

<cvParam accession="UNIMOD:4" name="Carbamidomethyl" cvRef="UNIMOD"/>
<cvParam accession="UNIMOD:35" name="Oxidation" cvRef="UNIMOD"/>

<SearchType>
  <cvParam accession="MS:1001083" name="ms-ms search" cvRef="PSI-MS" value=""/>
</SearchType>

Path /MzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/SearchType
MUST supply a *child* term of MS:1001080 (search type) one or more times
  e.g.: MS:1001010 (de novo search) 
  e.g.: MS:1001031 (spectral library search) 
  e.g.: MS:1001081 (pmf search) 
  e.g.: MS:1001082 (tag search) 
  e.g.: MS:1001083 (ms-ms search) 
  e.g.: MS:1001584 (combined pmf + ms-ms search) 

<cvParam accession="MS:1001083" name="ms-ms search" cvRef="PSI-MS" value=""/>

<Seq>MPSRSNSRGASADPASDALSDADAASSAVPGSASERSFPFVHPSRDQLTADKPAKRDADQEAFAMTEDTLPPVPPAPPPGEEGVPSSRFTSSEAFHDPPASPACASPPRRRCAAASPELEALGAFFARYACCLERVAVVDGAAECPGSLFGCALLPHVEASPAFAVSPAAWTSRWEADPFAWSGQGETRHGGALASRRVERRRPDHRRRAGDCGEKGPKRGARRGRKHGGARAPSRAGPETEPAAASPAASARQRLVQAMALPACAFLDLQAQQPSSFSVSPDGTPDPVYPQDLVSLDALRQGFPCGAPTGKSLGRIQDWSSTGATFWSRRVRAALDAFVLLPSWYGGIENRLLLEEAAVLLANTATCALLEAYAVHCLKRQAAAPIPRMYAAGHAAVSSQSSSFRHYPKSLTSGFSVFFGAGGQLPHPGRAPERPFSAPRVSPAARRVRDVGPAAGALRLWSQENSVFPHAVDFSPGRSEPQLSLDAGTGQCGDLGGEFGLCAVPAFLLGSRLPLGSFFSSLATSPHLLPLLLLRSHLGSLETGVFFPGGSAASSDRMGNRTATETPALAAVCSDFLSPSTLLDTSTFHERSRRGLREEERRRALAGAAGEPGEDDFFQLLLGSLGPERSRNLVAWSVAETDAFYLRCVYTLKTIVNLYMRFPPLFFFPRSMRGEDSQKQRTNGPDAGGDDSAASSAFPSHQQRLWALLLVILSGASPLSTDEGRQGGDSRADGDTLAAHFCPGEAVSGKREGRHASREPTPFAFGDAGGRAQDRRLGVRLTKTAAGSTLRLVAEALLCSALRNGCMSDILLTILVCLRQAVCDFQQASSAGLSAESAARPLISSYSTASQPPARPRGIPPNSKRWGSHYLEEFQLLTLFDDLSWTTEPSGLESGPDSPSLLLSSDRRAVEFVGKAADAVPLSRGSSGVSSDLARSPRPPGPRQGSSSSAGEAGTRRTASPLQIDSERVRDADSAVGRTAPAAHPPAPDSDEASGGAEAEAGEPRHRTAETGDSLEFLEVEDGIGGSPGRHAFGRDSSEGSGASSEGASSFLTSSSSRCQPSSVSSDLEEAPHWRPRNESETSSPRRREGRRDGPSGRARALRCSRASPTWVDDARGTRHARDDSSSSAGTSEGSQSVGTGSLGRGHLSARADSRRNATREAESDPEDREGARGGASLIGGRRPRRWLAPAAADILFVESRGAADRGPARDDGDEGDDAGAHAHRRHRGEATTFMTPVGVRVRSSQANCESASLVAARLTEDSRSHTITYFQLPSGVEPEDFDLISDIPAVSWPLVSQTRLDLPQGDSGLGTGSGSSSSLARRRSRARGDGEGVSGFPSSDCVDARVVCRYTAAFPSSSHSRTADWCGVPSARGRWGAQFLSEGCLPFASSPSVVDDLEARLENEAANPLVPSPNAWSPAEGVAARFLSQTLQGELLDALAEPVCTITHTVAPRAPRGSLLGPPVGPPVSRLERPRAVGSAHDPTRALAPQIASASLSPTRSDDDEIPARQTPRHQRDARRGDSSLPRASAPRSGRTAGGSRAPSEGLRTLQQLQRQQRRARLAATREAFLTGVHVCQLLVCEKISSALLAEGVVEPGRWRPASDALVEVGVLLGDAHLAPYSATRVRTRGPPPVSRSRNAGEPAHPGGSSEDAEVKENAGSSSDRAGRGARDQQTGGRDACGRPDAAQDSCMQSGGSKETTWQEKLYCRRAAGGGENRLGGTLCGRPGACGIRCDGLAWTEWGEARSARHGRASRAQGDCRRDETETRRRARGTGERGGYLHLGRRWTEAMRQGERLEGGKRIWCMTLMLNIEEGELDVFLDGKLLHTFGRLPNVSSACRGSEDSSSPLTSTLGYRFAVSLSSPSHVVGLVPLPRLSPAELDRLLNHHYRSSRALLPPADWTTKHPGALMASLSHAALRLSLKAKLTRDARAAVRGAAATATCLSPIFARGGGDSRDSRESGGAPRREETAEASSKGEASASAAPAIHIGGAGLTEWIKADGVTLDLLRECLGLAWDLLCRRAMHAAAEKERCQVAGGSGKEPDGTARAAGRLVDAQNGSATAPSVGAQGDGARGQAGDHKAGSESRGVKKTDSSSALPCPVVSPRSTFDDDAAMGTFYCLLRLWALLLPSAPLPPASKDASHPASSAVCQPWNTAPRPCARDPVDPLWLRDVLVRVVSSAASQPHAGAPPSTRDCEAWADLPLPVFALAAASRPGAWLVSPRDQLEGLVESRRVNREDESGEGTETPGGETVHTPTQRLAGGSRPRLDAAFCSRVLSLAPRWRRLVVSAAAEASTLTFCRALLLAPFLVTEGLDKCFCSLAFLRVAHRSFLEGDEAAGKEDVANLEAAAGAPVSHASPQPACALLEDAGEAGTWAQEAGGEEEARRDAETKEKDRDGDPEAEASAGGLDQLLCATLPAVVAALEDFHACVYAPLLPGGLRECPHSPSRDGRRARPVDSPESSGSFERGKHSSADAAPRPSSLCGFELASLASRVFAALGVLGTDGGVIALATAHCPPFLLLRLLRALLALACPPASVLLDCRETPALAAGRAYREDGAPGARGQSEAARRGESIPQVQGSERNAGPVLDAVGRLTRLVVRPLRRLLLQFFLCVRREFLHAIAEEKEEQMKRKSDCERRQLSQLFGRQARAAARHSPGNRREKGERTSGREGELAGGNFGSEASERARQGLTSTGGPRDELANRRESSPHPPRGFYVGSLADSDPGERDEDVDRPPDQVGDGSRSFVPVRVSRRAHPHPNRSEGEESGGAKTAEDSLPETPGPFLDPAHETPRRRLLPSISASSRPLRDKLDLHLDLLTAATELTFDALSSEAEQLSVPLPSFSSSQGASFAEGSVRLRLKCSERLLARVCKLVVYQIFLLIKFRKQQLFLAVLPFMSHTFLSERESRAESQLVRLLGRLDVFLVSLLPRLLQFAGRLTQAAVYADLVVALCTSGAPDCLLLQASRCDRRDRVETLAAETQAEALEAEATAAGDSGDADEPPAGVAEEETAVNRLSEGQTSAKDSAGAAVLVCWPDALPALCEALEGRGGRSRQRPRTPGRRRNPPTASPSSSGGEESDTGSVDEDRSWLRESLFMLPTASTAYRRLSQETCCVYLLETTHPLVRSRPRLRGWLRPAARTPRPGGTGAHASSASAPRDSGSAGAESLDADQRVFFGVSQADSAPGVLREGEGFLGLEAGMAPGLAHWLREDEEELCRGEGAQRVKIKFDPRSNTCDSGAELHIRVVTCHGVKTHQCFERNFPKLKFRDVKSIEFDFGAAYPSVDWGFRCQVEAYRKSSRHATHPSLELLLVAYDASFTLIHHLVEDLSPFLSPVSPPSSSTRGSPSFGAAAFAAAVDALRPLLLSQELVFSRPSTSAPSVRLFGPQSRASPSSPCSLFPSSLFPSLAADAAPTGCLVPWTECARSLYVAASEVRRIALDCSAAAQDGLSSPPHLPALFASHEHSLLSSLSPSGSSAVSSSTGRSVSPSSSSGRLNVALIDFVHGRSQVAKAIIALGDRFFSSPLSRTAGPPLLPGGFAHMAAAERAILALSLLLQPAAADLFLSLLSAIQDEAHLEAGDGAASEPRGKETENGAKGAALSGSHRSPAETRPPEEFSDASAASPFPAASPFPAASPFPAASPFPAASPFPAAPPVRELPRALQLLWRLAAQTARLAVHKGAQRFSSLRSEATEPGGRDGARPSLQATHKPALARRIAKNALFLLAWMRLSPTAWAARKKQRFAADRPLPLDPMSLRAWLLNDTTLQAVLRVALKPCSEGAALASPASQLKHFGLAVDLWNSYNARLRLAAEALIFVLEGLQTTVSLQGVLKRCRRGLGATEASEEQADAEATEAGEAQRRPRGSRRRHEKRMPPENGECIQWEGYARVGELSCLAVDASWRLLRFLDSLAETLLGTRKDAKCALVPLAAPSALPRCFVTDYERLLRPVLSFCGAPFAPAQTSASSFSPLALPGLPQFLLQTVLLSSSPSSFSSLLNEGSFALHASPADPSSSGASAPFAGSAALVAALCGVTETLSRFLFLSPSGPSQPPSVFNPSYPYGFTSQVAALSRAWLAPFLLSLLVLVTSSRCLRLQALGLWAAKQPKDRKEKDALPEEAAFPGDWRSRRRLLDAELLHETTEQARRVLRCVQTVVDATGVGLRRFLEWQTPKRHIRIPNFGPPAASLTEVPNGSLGESRTDEGGFWGAARRDLPRPDACRVSKLRAHAPNRYEGDAEGSCPPSSQGIRRRPASTLSQGSHVRLGRPPESSLDSLSAPQSRTRRAPTGERALSTRGLPFSPDRAAFPLSYLPPRGLPPVSYSDALVEVALVFVPCLSASRDSSRRLPASPSLRAFAQRSAAPGTHAAALLSIPAHGPVSKMLTRHFRKVDQCVVFVDAGGEDDMEIERESQANKEANAGWKPPTCDASRSTPLHQSRSESGAQPALLASSSSSPLSASAATTPHASRPLKPGQPVRVELWVRTAGQAFADLLASDGPPGGSDVYAGQRLAGSSSRHRGRRVRHSCYALVTKKKAAETLHTDRRQDGLWSGDSQAVPHAAGERRTADGDSGGSSAARLGRHPVASVTGSGEIAEDHVGVFPSRRREEGGDSDRPAFVHRGRGQPLWTQADPPPSGGGLESVPEGASGPVGDAGGCEGTGPNTRRTPSMRARFLSGEAEPSPAHWGTSAFLLAGDAPAGEAGRSARQPRALGESRERAEGVSSTRAEGGEAPAPDAPGGSGDSGGETERETDQVWWHGGPESATTTKIVQLAETKGGAPKWMGTVPFVRLLVPDTQAWHAAAKRALLSKTPRLISCSGDRMPSGGVQVSRAVVARVRLSRDEERAWAEAQRARNGEANKRAGRQVPALIVAEMGHVSELTADQVQRDFESHIRALADSNADPARRSPSPNPRRRLDTLPASSSSAVCTSAAFSASSSNSASHSEAGASAASTAGRRSARGGFAPTPRSEKVLTLRQQCCAALQTLDALGMQRTWLHATAAVSEYLWMSFRAAVGLALGPHVRLISHFLAAQSPSAPREAQEPCRGVQQSEDAGETASGRKQGRNTRGPRGRQEDRHAVSPQRSSLGALSPVGACLKHFARLLLWSVEHLEHASAKIGQGEATGGRRPRPGPSAGERGESTGTAEKARRKAGLARERNASCLSLSACLRRVLAGGCSSGSATDSDSESSNVPSTPPLPSAGPAPVAALMLRLLDVASGLSIDVEKRSPTPQISSRAAASPADPSPSSPLASASACFRASQGSAETASLSGEFSSDGSPSSGRSPLLGLHIAVQRYFHLTPTKAPPLLPEMLLSGLGLGSSYLADLLWHTTLQRQPASPPFSPGPPGASAASSPISGNEGVVVNRCRLSPACLPALHAALSANRRLLAILDHAEGERGFRAPGEGAECDQGGDGRATRERRTAPANGASSRSDERQTEARRKRRRPKTLQPGGGASEPDEAHTVSGGCSRSSAGAQAQRRAEGSRGEAALEGKGREESQRPGRAVETKAGPWVTWTEQRSLCLTAETIAVALLQLLQWVVEFRGVDREDEDDCHVQALWGTVSADGAWADSGCCLSQPGASPQPDSECETDADAPTPVGSRRRGPGGAHERLWMANLLPRLLATSVWGRPYLGRCAFRFLRLLLLARLRCVLFASSSPSVAVGTVDDTGQLRRRLGAVAAILPEPAVLAPLLPAPPAWLFWDLTGLGVSPDKPREDPVPPGGDETAGLAGEVDAEIDRTPGGFGDEHGRWMQTKWEKTRTVPGRRSATDLPQADGERTETQCTLSGGEELAVPTHAVSDSRTESETVPFSLASSPAQFEKAKRREEARLAAPSLSPAARCPSVLWSAPSLLQPVVLRASLPLPLAGPCWYRLAVKPGCGWFKLTALNGFSVRRICLGQAKQSGIKHADLMACIGLEVPTLRAGKDFGFKSQVTPLGQALTALERETLQKPSGFPIPTASFMDIITLAKPEKNVLKIRVDGKGMWNVPLLHPHVKINIASSSQTPSPGSLRRKAGDRGPRAQRAERPDRDATGHGRRAASRAVFEGGERAEKTTKRPAFAAAPFESTRKRRGVDRSLPQLSTMHELHLCIVTQVCSKDAFQLYVHRGGGEIDKSLRHHRKLNGLLRRVSHLHSTGLRGMAALETDPFLSDFWPVPLHQLPALPACNGPATLAFSAYALPSPSTFSPLLYRAPVSRALPASASTFPPDSSSLPGHVEPLLPSGSSAKIVDVAQASANSFTPSDASAALWETRRRELGVFASRAFDSHAHLLRWRWTCLFGDTLLLRQSVHLRRALLLGDLSLRTAKRQLLGERRREPADPTNGARNHRGQVAPSAAGGAAAGLAEPRRALVCDGEEPRSEGVGRSLLSGKTDVSSSPRRDANHREDAEGNGDNERASPQRDEEEVLGELLADVLNALADGLAEMEAWTTQGVRPQPLPFLALLSSSPSGVSFSSQRNATDLPSGLLGEGSKEATAREKSREGETAEIASQLAPSPARFFHFAHTQASAEALNRLRQVFSRLSALLRLFVFDGAAEDAESPTDGLPNVTGESPFTDFERLWLSGTFQRRLCESLLEPGNSEGRGGPESSRKKRDDPTFEHVFARSWFPRGVRATNYWQILTELSSPFFSEHRLWRPFFLLNAPESAEPERGLAARFGPVGAPLRRPWKPRSLARPTGPDTQNKDERAETAARGTEMPRSTPESPAGAAPRARSEPDRAGAGAAASGNCSLPVSSRVPEQGCSPEERRPERSHGQADWRDLWAMACDMKNAEDGAFLTCLVRLLPSSGRRLLLQKLRGNIQQILALCAKCGDLHADAADLPQHACFSEARLMRLSLLASCLSVLGAAEAATAVAHREMVQREEDGASEATVAEVETKRETENLDEGAAAHVARAAGGKVEEIRDTPRSPPSRSGRGRNTSLSSSAKVRDEREDDSATAKVTLALLTAVAPLVAASAPFLRRRSCHSEPAPSLNRLGCVADVAQLCAVKADVLLQRFQLLSYLSQASGYAALSVPLTPPLPPSSSAPARAAAGAAREAEKPGKGKGEEARDTATRASGHGSTDDEHPQPEKGGKGGMERKKRSADEARRRQVDGATCACCGVPIAEPSKANAKKAKRESPRRASSVSACATSPGGGLVTNPAALLSSAKAGAETVTVNSQPEGNLGDERGRDDLAARIQTGGFESMRQELLDAYDRPWEPSRRPALIRVALLTDLLESWRFLPPPGSSARHAFFSLLLRLSRATARVLDPRRRDYGEDPDGDSGDAAVASAVGRAADLDRELWEGAVTWPQVFWLFDQMPRFLPVADSSRWTSSEVTASVLNRLASAVSLSASAASDAASSASTAQNQARELPLTLAGTWGLYASSDDIFRLGPDPSAISSRAFLRLHGYASSCITNTPLASSACSSFSALASGSSLPLLHCDVDSADRSQHSTFWKPVVTDLEEVRGHPLDPVDLANHFFMGEFTRDGSSLQHAALAGGSGRVTGGGGAPRGPGGAGGARGDAPAGIAAGGVVEGDEEDASAVHHSPLAGGGGILVGHRPPGAGRSDDGASYPTHALFEVEADSVGSWSDQSEDDEEAMAAASGGHARGSRAPGRPGDSGGRLEGEGDDGRPEGRRRGSAGRDGGRRSGGRASLAGGDGSARSGGRRGLEVLMFASSEEEEDERAGLGDERGDSRRGRFDRIRILAEDDPRDLDEATELLTDEGETELAEVLPGDDDEPLECDAFECDDPLQGLLYENREVMEDLASMNLAFRSMPPLFRPVLASRLVPSLLVRPLWDRFSSEGYCASASDRQNRFPGGDEIRGADMGNAAGVVERRRNPRARDAASGEGHFLPCRDEEDESPSLRLAMVVHGGTGQMRHFEAGLDGEARAQVLLERPSASLPSAASTSEASRVISFVERYRRIAEGHGSYRTVYTADSQRQPDGSPAVAHFRVDRSAGLVPGADSRAERVRPEPPSWRRQRGVYEETRQLLAADGWRGRGGRLEASEPGLSEAEAGWRVQSGQSGERGSGRNGEAGFPPPGCSSFSFGSSSSDSASEDASLFDSEDDALSDGAVVVAHVLRPLERPLGGAAANRSGSVPRGREAREDQRRRRGYPRPRACSEGGGTCLGSFPPLQRSLSSHVFLSSATQNGRTHFAHSSSSSFSSSLGLQDSNNGWLPDIAWLRGSCADAGFDRLESLDRLESLDRLDASAAQSGLSPPLSASRAFRTLPVQDPPLLRSPSSSSCSALASRASAPACRLGGEDEGDAHKLCCAICAWPLCAGPAISDEAFAAAQRQFARRQRGVRPSRRRRWRKGRERSGRAAGGEKEIAETTDGHGYDGEDELGTVSDVSQTGEKAFVLGASESNVRWLLASSAAFSTAPRTWLVRSRPLPRSSLAHGRFAELKVGESAHEESSFSATAHSDFPSLSVAGEHEARDGGAHLVPQANGEARKARETQEEKATTVDPSAVVVAPTKANELTRVTGHAVEAHSREAFSRITKFSHKSTRAQCRQSVEAAGGDLRGDVRTPTDLHDLPLVSASLRETSPVLLPSFSTLAPLPVSRQALTPQFVLDARQAASDGEADTRVFRSPRFRRVCSFRRKTQQLAGDERRRTPRTEILASMDDQKVGVNGTDVNGVADEAAAGKARRETESVDSGHGGRYKKPAGGPGKGRVGRRSGDPSAQFPCAICRYRGFTCSAQATFTSRLRGPSDNERRFPLWWLQGSFSTARGPRHKTSHAASLAHVGDDGGRATWPETPEWIPLFSRFTAAVARCRRPSFSQVDLEGSGTAQLSGGDRMPSPLPLRPRTLSSVYLPSRRSACLSASVAGGNVRAASAFFARDQKSFRRAGKRSATPGSAQRALDKESERGPALRSPQVRALRSGRLSSAQDGKSRLAQDHGSKRQGGAKGMKPFDSEKACFPPVDSEAARSFSLPSGHAGTPGAFSSLGELHRLFWRQYYAAQDEALLLMLAPFLGGNPVSLSNSWPGGRAFFAANDVPEDIELSSLADVRCPRCGKTLKNIQGSGFEGKWRCDGLDQNGFCVASLTDYRLWSAAARHRCHSDDFDYCQACFEYKARLNARKLKWLSTNSSRLLWPSHRPACPSGPFLWQLGSPRLPEEHRRRAEEAQRRIEALVKKARERQERPEVKADSAGDRRPELGEERKSGKPESRKASTAETDWRGTRDDAREPKGDRGRDPEEIVSRNASASSGPLPRRSRRGERERGSLAFHRSSSCASSAASSGLPSLWRGPERLPAVQSPQACMQSWIREATQLPLLAQRPRSSSGNGEEVVLRDGVVLLIPSRLPYLPPPPCNPVLLDGLLTSAPGFPESLAHRLLRLGCTCLLPLFFKNFETLRIHGSRVLPAAAASDAAAGDALQAVGEASGSGIAYPPPFPATARERRPDGAQPRGGDSRRPAGGEKASRPATHLTVSLVAEEAVWPLVIQGRFAGSGDCRSIPHLKKDIADHTHCETEGVLLSCFQNGRWHGAARREETLRDGGDGANRGQGDFLCGPFNRQMDGQGDGKWFIDVHKAQRDPQHYKGTVGYNGSVGYWNLDTDVPGHVAPAFLAVSGHACTPEVRNKAILFVSSLQRHLEVFLPANQDELEAQMNFLTEAAESLHAAGRTGEGRAESTESEDQAGERGRRCPDRTQNATKETPREDDADDVAEADEAPERRKTGKRATGSKAPTKGRSRGDAERCDASEVRASARSPSHRPGEGEQPVDVGNCAVSSGEAFEVHLCPACELQQQAPGDSLQRSERAARERIVNPRASSASGLSVEEEDEYLALKAWEANADPLAAALLPVDALQRQQMSAAVRCYQWETALQSQNALVQLWLLYPSLALDSWPLVLRFIYDAVRARPSMHRVLVELLLAVVKAAAVQGRRRDDTEEGTTDTSSDADSSEEESAEGDGFDGRLLGRGSERLESRGTGSMGAFTSSRFFSPLLPSLSSSVLTSSRDRDRETDGGRAIASHLGALALLHLAAIGLLDRHSAEQAEAYRVYRAGRQQQLALQSVSAQSEDACSPLEGVAFEALSQRLHLDGAAGHFVSLGLSRAPHGDPDGAGDGARARAGVSVSQLFRTQEETQNAARERGAQRRREGNREAKQETSSLLPESRVYAGIAYGVHRPWPAACSRDIFSLSPQPIVESDASTTPRASSLSAGAPSVPSPDCDGGSDAARGSGELPSSDEEEGRDRERRVRREPDDASRPWRVADPRPRLPVAFCRFQEFAGGAGQSGAAQQLKYLNPALLVDCLHSESRHPYRPTERGGRKTQVGVEEFILSRPVNGRRRGEKRRGAGEAGDGERAEGAAGSAANREERRDKNSPEKVAVDRRRQGRETKGNISVDIAMDPGFDWARGFLIRFSRMSCTRPGDSLRFYAHPADDICVAACSGASERPWTSPVFLPGFRFSYAFHPFGLNSPSAPLPNPMCGSNSAGLWMSPEFTPLTFASPANDLRADDAAAARSAELEAVERERNGREEHGCGARTAQSDERAAAARYPYPSLHASGAPPRTRSAQRAVDANGGPVEGARRRGRLYTQSASMLEAARGGRATATDLDSHATGNCGVEATESRPDGGTEKPRRRLSDRGIEEMEPAHAMWGWKFVVSVANRAEVLQHYTNLPAPFPSPAAGRALLEAFPGTQERTSRSVAETGDKGAVPKPRGAHASGGKPRKKRRRRAESAFRSLQSSLFLDLFQPSVDLTFIRWLVEDVGGHPEVREQAQTRAAVSLLTSRSEDTPLTETFPDSASDSGASTAGGERQKDAREPGAGARNARELRTDAKWREERAVRASLAHLLACVYHPNVFQALVGLAGSCATLEGCGPALQPAAVFLVKRFSQLAPWLQGPPRTHPQRQRRLRAQARRVHCDDPSATSSCLADSERHPEVQLGSPFWLSSQESPSPCTVGRREPGGTNTPGLNCLETCTSSRLSPPSSARSCGSAAPALHASSPSSPLRVLPETSEGSLGPQTPSRSFSPQATAPAIWSRDAGSSSESSSPDAACSLALASSSQQRDERDAERDVAPAEDEALALSARMRFFFLLLFMEIAAQIRVPRVADSVFESAGVNSMYTSQSETQGGSSALPLSSLPPRPRPLRPTQQIILPPLAEYVGQVLAVLFSACKCAAACGECGAEAREANRRRQLSAQRVTWRLSDIRLLCEKAEREPRSNPSRTSRLDGPSSPRCRSPFSAFASEADPSNAGGRRAHPPRSVSTAGSNRLSRSTPSCPEEPHTTSATLSSPFSACGDRPHDHSYQNSYPAFRSQSPSGPASSFGPASSSPPPLASSDSPPSQCSVSLLSRWSCGDTRGVSSSASRDTRWCPHAASSPLWLQPGPVPLHGGGQPPCEAPASSGCVGGTGFCVEQAVKELLLQCKVLQDLRGLEGNLPHSQGVPFALFLFEFLQRLTALRGVERSRLGNETFWECKRRLGAEGPGEGAARSEVCGRARQRGPDPSQSTGGSLAVSDAFWNGQYLLDGRKCRGCPGDARSSDRFEVDFERFLPLLDEESQHMLLPEHLDLRKALWPTLWRIAEKRRQLARTRKALAGTHPTARGPAMEPQLGGQQASVAQRAGGQGGDGSGATDARTHALERGNASRPAAANLGLSTPASFSISPSFSLREAEGAGGDASEADLARDSRRRGSERPLSARNQCEGGDSSPRTGRVLPESASSPVLSVPPQWLSTERGEAAHISGRMQDSRDRSDVPVCLSSPLQLSSASHSFQSYTPYKIAFSASSPLALPLLAGLGSPSVASDALEAILPVSALDESTSCQARRAGQSKRGIGEADEGARHPPRALTAPALPLAHARPGAVPVFSPLAVRLDARELRRRLCLRWGVGPRSGAIGDGRAEPDSLGGGVCLSDVRALDSFAASAQTSRQALASWALERGDSGEERTEGCEAGDSGKGHPPFTSDPVAFLSRELALCFEADVRTIDLSPYAAGAVISFCSSPSQLAPGDLLTVYARPRGAFCTRSRAPGPQSSRVSPAASVSPPSPWIPVVEMSNYHADCLWYATDYSPSLSPQLFFPAGSPPSPHWPEEPSIANTRPRLRDGDKERDRGTGYFALGSLAAAVRLGLLDATEAAPFCPASLTKREERTKDDVCAGSDGAQKSPCFRGDSDAHVAGKAARPLDAARALATAAGALAIETTPLEGFPEEERRVRGEAKLAASMESAQVLFSRPASFLWRLPPSLAHAPSVNEDQNSGLGLGTEKRVETRFLKNAVGLLTERDEDVWGTVRRLASHSSLARPLPSHLASPLPVSSRGQPSQPTALPDRSRSFSSASLSSASSLVLPAPGSSSRAPHPPVPRSYQRRGSGHPTPAAAPPAQFTRSGTRSRTFSGTSVGRSGSFGALTGGLSSLPTTAGRRSSYCAPTSSATSAATPSASSLVGAFASQNPVFAMALERGRDERRRDREAREEPDAGGSGAVPASSSSGLCRRGRRHGSLAEAARGGLQGEGRRRGSSGDALLALSSLGETPQALSWGSSSATALLPGRGGRSAGACMRRGSFAGRTATAQPFGKESSFSSDGGSQRGSAEASVRVSGLPSHVGAAPTDEARQNRDEARVGASDTIHLVSGALIPRDEFLRAGVWRVEFTVGWRQNGKNQPLLAPDEGSLPALPRCTGGDEDGQREDALGWHAGPEFGWAPLTHAVSPEEAAVDALLSELLGTRSRTTRSAETAEKRSDPKGVEKRPEPAEAGTRSSDDGRTSTNAQIASEADSQSRNSPLTRLSSASSPPSAAPSFTVPPPASRYFWLSCTTQVVSGSGVVSPTPRREAEGAWASVSGSRRNRSCLSSLSPHQPQAPHAAAPATEAAADAGYLSLSAVGKAPPRFDRDEETQERRGDSDGEAQEPCVASRLTLGPGDFHSHPFIPDPPIYQRTFALAEHLNRSYPPQSFTPPCYRVLPSPGLLRSPSPPSSAPRSSFSSLSSSLSPAASGGVCVHPVTSGEPRVAAYSDVMARVHAHHQQLRPSQAEVRGVWCVSPHGKQTVQDTVVAGDWIDSQSVAAVLTACASGLHPEAAEERACSGSGARRDRSVGGDTEDAPTGEGFCRDDAQLWERNAEGRNWAFSGPALAERLTPEDVLSRAEVLCSASSRRLLHFGRSLELSPSRACSAASEFPSRSESPVTGASGGDVETEELRTLRGRRTRFSPGRPQAERGRAPLLEKEDQSRREDSNSPAPHLAGARGGLAGRGSSRGFQDEGPPRNGIDLGGGGEGDNAGANGEASQPRRGEDEGDQVERRRARRDATQRGDEATRRSALRGEIENHFLEREKQSPETGRSYFRTSKLTMELSFTPDLDRLRDLHAAFADLNTAMAEAHTLLASSPPSSCSSSSSPSSFAGSCSGAVSVPSSSEARQAMAARVARLVKRVQMLQQLGPRDEVRCSFRVESPESERGSKPNQEDETQSEKYNMTWHVGGLKSLLGAGRGVALCPAVKLGPCATMLQVTRVHQPCPAPRTLSLVNCPALLVTHCSSLKICLSPSPYRTHRDWRLLNALPADAFLDSFAPRNARLVLLGKGRERLRPARGAGRSGRQALESRRWGKATERADRTQKETSSQAASGVSPSPAGAPDQAGENVAVDEHGEHGQGRRAWRRPACGGETAGEPAGRSTARRGSAAEREASGKRGASGERLSVEPQWREHGEHEGEGVAARKEIVDKKNQGKGRREENGGERGSRLAHAAEACSSSLPPPLSAVDPRPSPSSSPGPSFSSLHAGRSFPRALPGEAGDAVRQGGLGSGGATAHQRVEGMKPSLSSPELRWGTAANEDQFRCFFAPFPAFRPVSQSATRRRDGATDAPLLQPTPNALPHFASRLPECGVASRGLDVHSGAEGGPGLHATRRRHSREAACLPWGRQPRGDAARKGPTDGERSERSLVGSQDRQRRMSAVEASSEAGFSPFASSNFDADGCCFEGLGDANPGQTGPRREGTGDTPEGSGVLPSWESILFEQDQGLTYVGPPGAWWRDPERLSGVSSTARGRSAEAESARETEASERYEGWRLLVRQLIPAGHQVNAALAAEEAVGGELAAAAGQLAHALLLNDESRARRRRRNPETSSLGFYSSRAGGKTPSAQDLPAAPGEEGEERSSDRLSRAWQEPQEECSASREGGETESKVASESVASAERGSNEERRDEIRDSAKVEASGASERASRSPNFGDAESNASLLLSVTPSESPSSSQSVALFSHSGDVSQSRVSLRSSPNAPPLAQRPPGRSQPASASESVAASFFGASEMSRGSEPHFASVQEGLLAPSQSLSRFAQASGSPASPPLVHPSSTSAPPASGDEGLLSASPESAPRSLRAPLAGDGPSSGRHALVSDSLSESRSATDASAARDAASLSASPLWQLPVSFSPSVLASLGRGRVSGLLPESGPQRGLHARKRTLWKALKAALRCARIRVPLQGVVRDLEVRVGVQSQPWPDELLQQLVDIAAKGNASLRDPKTGPAVRPLPPLLLPLGGSATSPEATGECEVVARTTVEGSHPRPSRRKPGDGEVANADRVPPGDVGRGPSSLGGLGLDPGRLLSDSTLFCVSSSLPSLPSCASDASPSAFPLDCSDPPHASFSPESPACVVRPFQSAVSPDGALRVSPLDIWTWHLPFFPGLSSDAVAAWLLRAQKGQVRRATERAREAREAQNRDRRGRQGAGGLAGEAGEEGTRARRRQEGQGRDASQVEAEEDSGQGTLGGRRRRHPLVGSPVHEGDRSGDSGASEPSTESPFGAEASASPPRLRSAEASESPRFFVDPDEGFSDGDVTGDEAPEERDGRIFWDDVDTESEHPWPEVAPDASLAYSEPYFTEDYADDGFQRDWRLEDGFEAQDAGQETLVPREDAPMSRVSSGPSDGRGRDGGAASLPGAALPPASGPSGSSGGGDAEEERSSAEEDEDDVEDAIADEGEPLHPPGGVSGIASSASDVFTRGYVSAVDQLASELWMLYEVLVLRECVKRVASAERRKRERGERHQAQRHGASRDRQIRSPSAASPAVGGVSAATRDGASESQAESAGIGRARAEAPETERESPRRQRGRQAESGQTHRSTLSSFPYYEGALAAIEEDEATVLFDRPSSPQSGPTRDAFGRGGLEDTRGEDAMGDSEARSSGRVEAEASSERERLPQPRSFLTGSPPIYTAVASPLVELPSFCSPLLYQVLYEILLLFLRFGLARCAARRSSSARDLLRYWPPTVGDLRVALQLRLRYLHQVNVSFLFLSPFLPTVPPPYPYLYEERHEVHLGLAPAASLRGDSHARDGAETEEWGSGRSMRSSDPVAFSWSPTSHTGGGLLTRGGRIGKTPTGGLRARAAWGLRRLPPLAFRTRNETARSLRDAEENLNACQRDAEHDGGFRGEGTQQPADGRLRPPAESASLRVLPESLSSSPVSLWGPGSGEEREDCEDRDKVLVALSGTKALLLPAVKNFLFRASTIYRVHAIRQQILRLPGFTYAFRQPERPRQALAGDTSLLPALPSLRTPAASANSPALSGFLGLSRGAGVSAPRMSLAWEATVSLIRLHAPLEDIYVASARSGSLLSQGRSGSSATLVVDVTAPLPEAWGNVGGAAVLLDRNATRQTEAEGPAVVSGAADLQTAQIPGVDTPGSRGGAGWGGEPGDAATGELEPADGRLPGDTRLEKSLTVQLAKQLQHVDALKLVARERAFVVQLRGEGAQDLGGPYAEILSNLCDDLVTQKLVVECPNARNSVGNNRDVWILNPRLREFLLGADASALPGVQTAHPVGGWGPSGASGTSGADDAHRDAEDREGDFLSGAWRGFESHSRSGEAEDIVALGCQGPSDLGSPEASSASRWAPNLSPLPVLPLFPAEALAVPSLAGALDAECVDACGLFGFFAPSTSSAILSGCRRRFDPSHGVAGSAGAARFESETPNRRLRDRARASWRAWEANEEREDRTCFRLSSYGQHLASALFVVGRLMACAVLTQSPLNLSLSPSLWKLLLLQLPALQDVHAVDSLAAKQLKTFLACCGLAHRRRASPASAEREKRGDEDLGNASEATESQSVSRVDADRDKATLQAFAQNGWAVDDALGRNVELFLGGARCPVDDEDIADAVQAALLAKLTEGHEAAAWIAYGLYDLLPLPQVQATLTADDLRQLVCGDDDIAVAVLMRHSKVTWDNNDARERALIDNLWEVLSAFTKKEKQMFLRFVSGRSRLPRSWVSGDPSASPHKFEIHVMRDEEALEIQDASLRSVQIAENQTVDDRLPTASTCFFMIKLPKYSSKEVLRKKLKLAIMSCVDIDLDALHHDLDFAQFE</Seq>

<cvParam accession="MS:1001088" name="protein description" cvRef="PSI-MS"

<SequenceCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
    <DBSequence accession="Rnd3psu|NC_LIV_083320" searchDatabase_ref="SearchDB_1" length="661" id="dbseq_Rnd3psu|NC_LIV_083320">
        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="Rnd3psu|NC_LIV_083320 Rnd3psu|NC_LIV_083320 Decoy sequence, was | organism=Neospora_caninum | product=zinc finger (CCCH type) protein, putative | location=Neo_chrVIIa:3989308-3992771(+) | length=661" name="protein description"/>
    </DBSequence>
    <DBSequence accession="Rnd1psu|NC_LIV_123020" searchDatabase_ref="SearchDB_1" length="2986" id="dbseq_Rnd1psu|NC_LIV_123020">
        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="Rnd1psu|NC_LIV_123020 Rnd1psu|NC_LIV_123020 Decoy sequence, was | organism=Neospora_caninum | product=hypothetical protein | location=Neo_chrX:3202583-3213218(-) | length=2986" name="protein description"/>
    </DBSequence>
  ...
</SequenceCollection>

<SiteRegexp><![CDATA[(?<=[KR])(?!P)]]></SiteRegexp>

<SoftwareName>
  <cvParam accession="MS:1001478" name="Mascot Parser" cvRef="PSI-MS"/>
</SoftwareName>

Path /MzIdentML/AnalysisSoftwareList/AnalysisSoftware/SoftwareName
MUST supply a *child* term of MS:1001456 (analysis software) one or more times
  e.g.: MS:1000532 (Xcalibur) 
  e.g.: MS:1000533 (Bioworks) 
  e.g.: MS:1000534 (MassLynx) 
  e.g.: MS:1000535 (FlexAnalysis) 
  e.g.: MS:1000536 (Data Explorer) 
  e.g.: MS:1000537 (4700 Explorer) 
  e.g.: MS:1000539 (Voyager Biospectrometry Workstation System) 
  e.g.: MS:1000551 (Analyst) 
  e.g.: MS:1000600 (Proteios) 
  e.g.: MS:1000601 (ProteinLynx Global Server) 
  et al.

<cvParam accession="MS:1001207" name="Mascot" cvRef="PSI-MS"/>
<cvParam accession="MS:1001478" name="Mascot Parser" cvRef="PSI-MS"/>
<cvParam accession="MS:1001475" cvRef="PSI-MS" name="OMSSA"/>

<SourceFile location="file:///D:/TestSpace/NeoTestMarch2011/55merge_mascot.dat" id="SF_1">
  <FileFormat>
    <cvParam accession="MS:1001199" name="Mascot DAT file" cvRef="PSI-MS"/>
  </FileFormat>
</SourceFile>

Path /MzIdentML/DataCollection/Inputs/SourceFile
MAY supply a *child* term of MS:1000561 (data file checksum type) one or more times
  e.g.: MS:1000568 (MD5) 
  e.g.: MS:1000569 (SHA-1) 

Path /MzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ModificationParams/SearchModification/SpecificityRules
MUST supply a *child* term of MS:1001056 (modification specificity rule) one or more times
  e.g.: MS:1001189 (modification specificity N-term) 
  e.g.: MS:1001190 (modification specificity C-term) 

<SpectraData location="D:/TestSpace/NeoTestMarch2011/55merge.mgf" id="SID_1">
    <FileFormat>
        <cvParam accession="MS:1001062" cvRef="PSI-MS" name="Mascot MGF file"/>
    </FileFormat>
    <SpectrumIDFormat>
        <cvParam accession="MS:1000774" cvRef="PSI-MS" name="multiple peak list nativeID format"/>
    </SpectrumIDFormat>
  ...
</SpectraData>

<SpectrumIDFormat>
    <cvParam accession="MS:1000774" cvRef="PSI-MS" name="multiple peak list nativeID format"/>
</SpectrumIDFormat>

Path /MzIdentML/DataCollection/Inputs/SpectraData/SpectrumIDFormat
MUST supply a *child* term of MS:1000767 (native spectrum identifier format) only once
  e.g.: MS:1000768 (Thermo nativeID format) 
  e.g.: MS:1000769 (Waters nativeID format) 
  e.g.: MS:1000770 (WIFF nativeID format) 
  e.g.: MS:1000771 (Bruker/Agilent YEP nativeID format) 
  e.g.: MS:1000772 (Bruker BAF nativeID format) 
  e.g.: MS:1000773 (Bruker FID nativeID format) 
  e.g.: MS:1000774 (multiple peak list nativeID format) 
  e.g.: MS:1000775 (single peak list nativeID format) 
  e.g.: MS:1000776 (scan number only nativeID format) 
  e.g.: MS:1000777 (spectrum identifier nativeID format) 
  et al.
MUST supply a *child* term of MS:1001529 (spectra data details) only once
  e.g.: MS:1001530 (mzML unique identifier) 
  e.g.: MS:1001531 (spectrum from ProteinScape database nativeID format) 
  e.g.: MS:1001532 (spectrum from database nativeID format) 

<cvParam accession="MS:1000774" name="multiple peak list nativeID format" cvRef="PSI-MS"/>

<SpectrumIdentification id="SI" spectrumIdentificationProtocol_ref="SIP"
  spectrumIdentificationList_ref="SIL_1" activityDate="2011-03-24T11:37:37">
  <InputSpectra spectraData_ref="SD_1"/>
  <SearchDatabaseRef searchDatabase_ref="SDB_NeoProt_tripledecoy"/>
</SpectrumIdentification>

<SpectrumIdentificationItem id="SII_69_10" calculatedMassToCharge="515.329999"
  chargeState="1" experimentalMassToCharge="514.242" peptide_ref="GIGLR_0000000" rank="10"
  passThreshold="false">
  <PeptideEvidenceRef peptideEvidence_ref="GIGLR_0000000_1_psu|NC_LIV_020600_1026_1030"/>
  <PeptideEvidenceRef peptideEvidence_ref="GIGLR_0000000_1_Rnd1psu|NC_LIV_145070_441_445"/>
  <PeptideEvidenceRef peptideEvidence_ref="GIGLR_0000000_1_Rnd1psu|NC_LIV_120130_148_152"/>
  <PeptideEvidenceRef peptideEvidence_ref="GIGLR_0000000_1_Rnd3psu|NC_LIV_072540_650_654"/>
  ...
</SpectrumIdentificationItem>

Path /MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/SpectrumIdentificationResult/SpectrumIdentificationItem
MAY supply a *child* term of MS:1001405 (spectrum identification result details) one or more times
  e.g.: MS:1000796 (spectrum title) 
  e.g.: MS:1000797 (peak list scans) 
  e.g.: MS:1000798 (peak list raw scans) 
  e.g.: MS:1000903 (product ion series ordinal) 
  e.g.: MS:1000904 (product ion m/z delta) 
  e.g.: MS:1000926 (product interpretation rank) 
  e.g.: MS:1001030 (number of peptide seqs compared to each spectrum) 
  e.g.: MS:1001035 (date / time search performed) 
  e.g.: MS:1001036 (search time taken) 
  e.g.: MS:1001088 (protein description) 
  et al.

<cvParam accession="MS:1001171" name="mascot:score" cvRef="PSI-MS" value="13.49"/>
<cvParam accession="MS:1001172" name="mascot:expectation value" cvRef="PSI-MS"
<cvParam accession="MS:1001363" name="peptide unique to one protein" cvRef="PSI-MS"/>
<cvParam accession="MS:1001371" name="mascot:identity threshold" cvRef="PSI-MS" value="43"/>
<cvParam accession="MS:1001370" name="mascot:homology threshold" cvRef="PSI-MS" value="26"/>
<cvParam accession="MS:1001030" name="number of peptide seqs compared to each spectrum"
<cvParam accession="MS:1000796" name="spectrum title" cvRef="PSI-MS"
<cvParam accession="MS:1001328" cvRef="PSI-MS" value="0.866331351956052" name="OMSSA:evalue"/>
<cvParam accession="MS:1001329" cvRef="PSI-MS" value="2.0805267818349E-4" name="OMSSA:pvalue"/>

<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_308_1"/>

<SpectrumIdentificationList id="SII_LIST_1" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
    <FragmentationTable>
        <Measure id="Measure_MZ">
            <cvParam accession="MS:1001225" cvRef="PSI-MS" unitCvRef="PSI-MS" unitName="m/z" unitAccession="MS:1000040" name="product ion m/z"/>
        </Measure>
        <Measure id="Measure_Int">
            <cvParam accession="MS:1001226" cvRef="PSI-MS" name="product ion intensity"/>
  ...
</SpectrumIdentificationList>

Path /MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList
MAY supply a *child* term of MS:1001184 (search statistics) one or more times
  e.g.: MS:1001035 (date / time search performed) 
  e.g.: MS:1001036 (search time taken) 
  e.g.: MS:1001177 (number of molecular hypothesis considered) 

<SpectrumIdentificationProtocol analysisSoftware_ref="ID_software" id="SearchProtocol_1">
    <SearchType>
        <cvParam accession="MS:1001083" cvRef="PSI-MS" name="ms-ms search"/>
    </SearchType>
    <AdditionalSearchParams>
        <cvParam accession="MS:1001211" cvRef="PSI-MS" name="parent mass type mono"/>
        <cvParam accession="MS:1001256" cvRef="PSI-MS" name="fragment mass type mono"/>
  ...
</SpectrumIdentificationProtocol>

<SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="index=21" id="SIR_32">
    <SpectrumIdentificationItem passThreshold="false" rank="1" peptide_ref="VIDENFGLVEGLMTTVHAATGTQK_1@12" calculatedMassToCharge="2546268.0" experimentalMassToCharge="2547212.0" chargeState="3" id="SII_32_1">
        <PeptideEvidenceRef peptideEvidence_ref="PE32_2_53"/>
        <cvParam accession="MS:1001328" cvRef="PSI-MS" value="7.40729329987533E-8" name="OMSSA:evalue"/>
        <cvParam accession="MS:1001329" cvRef="PSI-MS" value="3.18593260209692E-11" name="OMSSA:pvalue"/>
    </SpectrumIdentificationItem>
    <SpectrumIdentificationItem passThreshold="false" rank="2" peptide_ref="APCSGSAVTGVDSPGCDGVGDLNVTR" calculatedMassToCharge="2547129.0" experimentalMassToCharge="2547212.0" chargeState="3" id="SII_32_2">
  ...
</SpectrumIdentificationResult>

Path /MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/SpectrumIdentificationResult
MAY supply a *child* term of MS:1001405 (spectrum identification result details) one or more times
  e.g.: MS:1000796 (spectrum title) 
  e.g.: MS:1000797 (peak list scans) 
  e.g.: MS:1000798 (peak list raw scans) 
  e.g.: MS:1000903 (product ion series ordinal) 
  e.g.: MS:1000904 (product ion m/z delta) 
  e.g.: MS:1000926 (product interpretation rank) 
  e.g.: MS:1001030 (number of peptide seqs compared to each spectrum) 
  e.g.: MS:1001035 (date / time search performed) 
  e.g.: MS:1001036 (search time taken) 
  e.g.: MS:1001088 (protein description) 
  et al.

<SubstitutionModification location="15" originalResidue="X" replacementResidue="P"/>

<Threshold>
  <cvParam accession="MS:1001316" name="mascot:SigThreshold" cvRef="PSI-MS" value="0.05"/>
</Threshold>

Path /MzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/Threshold
MUST supply a *child* term of MS:1001302 (search engine specific input parameter) one or more times
  e.g.: MS:1001005 (Sequest:CleavesAt) 
  e.g.: MS:1001007 (Sequest:OutputLines) 
  e.g.: MS:1001009 (Sequest:DescriptionLines) 
  e.g.: MS:1001026 (Sequest:NormalizeXCorrValues) 
  e.g.: MS:1001028 (Sequest:SequenceHeaderFilter) 
  e.g.: MS:1001032 (Sequest:SequencePartialFilter) 
  e.g.: MS:1001037 (Sequest:ShowFragmentIons) 
  e.g.: MS:1001038 (Sequest:Consensus) 
  e.g.: MS:1001042 (Sequest:LimitTo) 
  e.g.: MS:1001046 (Sequest:sort_by_dCn) 
  et al.
MUST supply a *child* term of MS:1001153 (search engine specific score) one or more times
  e.g.: MS:1001154 (Sequest:probability) 
  e.g.: MS:1001155 (Sequest:xcorr) 
  e.g.: MS:1001156 (Sequest:deltacn) 
  e.g.: MS:1001157 (Sequest:sp) 
  e.g.: MS:1001158 (Sequest:Uniq) 
  e.g.: MS:1001159 (Sequest:expectation value) 
  e.g.: MS:1001160 (Sequest:sf) 
  e.g.: MS:1001161 (Sequest:matched ions) 
  e.g.: MS:1001162 (Sequest:total ions) 
  e.g.: MS:1001163 (Sequest:consensus score) 
  et al.
MUST supply term MS:1001494 (no threshold) only once
MUST supply term MS:1001448 (pep:FDR threshold) only once

Path /MzIdentML/AnalysisProtocolCollection/ProteinDetectionProtocol/Threshold
MUST supply a *child* term of MS:1001302 (search engine specific input parameter) one or more times
  e.g.: MS:1001005 (Sequest:CleavesAt) 
  e.g.: MS:1001007 (Sequest:OutputLines) 
  e.g.: MS:1001009 (Sequest:DescriptionLines) 
  e.g.: MS:1001026 (Sequest:NormalizeXCorrValues) 
  e.g.: MS:1001028 (Sequest:SequenceHeaderFilter) 
  e.g.: MS:1001032 (Sequest:SequencePartialFilter) 
  e.g.: MS:1001037 (Sequest:ShowFragmentIons) 
  e.g.: MS:1001038 (Sequest:Consensus) 
  e.g.: MS:1001042 (Sequest:LimitTo) 
  e.g.: MS:1001046 (Sequest:sort_by_dCn) 
  et al.
MUST supply a *child* term of MS:1001153 (search engine specific score) one or more times
  e.g.: MS:1001154 (Sequest:probability) 
  e.g.: MS:1001155 (Sequest:xcorr) 
  e.g.: MS:1001156 (Sequest:deltacn) 
  e.g.: MS:1001157 (Sequest:sp) 
  e.g.: MS:1001158 (Sequest:Uniq) 
  e.g.: MS:1001159 (Sequest:expectation value) 
  e.g.: MS:1001160 (Sequest:sf) 
  e.g.: MS:1001161 (Sequest:matched ions) 
  e.g.: MS:1001162 (Sequest:total ions) 
  e.g.: MS:1001163 (Sequest:consensus score) 
  et al.
MUST supply term MS:1001447 (prot:FDR threshold) only once
MUST supply term MS:1001494 (no threshold) only once

<cvParam accession="MS:1001316" name="mascot:SigThreshold" cvRef="PSI-MS" value="0.05"/>
<cvParam accession="MS:1001494" name="no threshold" cvRef="PSI-MS"/>

Path /MzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/DatabaseTranslation/TranslationTable
MUST supply term MS:1001410 (translation start codons) only once
MUST supply term MS:1001025 (translation table) only once
MUST supply term MS:1001423 (translation table description) only once

<cv id="PSI-MS" fullName="Proteomics Standards Initiative Mass Spectrometry Vocabularies"
  uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"
  version="2.32.0"/>
<cv id="UNIMOD" fullName="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo"/>
<cv id="UO" fullName="UNIT-ONTOLOGY"
  uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
</cvList>
  ...
</cv>

<cvList>
  <cv id="PSI-MS" fullName="Proteomics Standards Initiative Mass Spectrometry Vocabularies"
    uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"
    version="2.32.0"/>
  <cv id="UNIMOD" fullName="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo"/>
  <cv id="UO" fullName="UNIT-ONTOLOGY"
    uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
  ...
</cvList>

<cvParam accession="MS:1001088" name="protein description" cvRef="PSI-MS"
  value="Rnd3psu|NC_LIV_111720 Decoy sequence, was | organism=Neospora_caninum | product=forkhead-aasociated (FHA) domain-containing protein | location=Neo_chrIX:1702443-1710709(-) | length=1155"
/>
</DBSequence>
<DBSequence id="DBSeq_1_Rnd1psu|NC_LIV_080090" length="16207"
searchDatabase_ref="SDB_NeoProt_tripledecoy" accession="Rnd1psu|NC_LIV_080090">
<Seq>TPLRAFARSEISNPSLIVLDDVLSQSLSSPGSHLERLLPEAEPGRGAEIDTKPHKRTTAFFSLEHEAEAWPPAPPTPPPGNQYAPIDRVGSATGADDPPTAPFALVPPRRRNLGLAPELFALGSQQTRAGIYSGRVGATQNTGVGPSAQLAAQANPAELDTPSQLAGPGSLVARALWAPVTFFLENSSRSLSSNSSRRLARRRPMERRRASTTGDKGPKRTARRIRKMAFLREPGRLGPLGGPLVAVPTEGNRTRALFYEDGPTSAEILSVDSTPLSESHIPLHDPDPGVPGAEDNFGAVREEVPVTCPLEKHNDRDLMATQDAAQELSRRLRTLEELASVDPAIGAMHETRAGGDVEFLAVAECDDSSNIGELSMDNIKRILEHPAPRSAGTDCQEVSEDGSMQRVGPKLASGGNNDAYDETALLPDPTRDPGRPVSIPRDDPGSRRERTCLPGEAIARLCSAIIQGGPAVDVTAPMRIHPTFTGMDTNIHDATDEAGDSFELAPSAGGAWREPLLGFAHVNLLQPSEMPGSAVRGAGGVCNHTVTSPLDLGMLAVRLFSRELGVEPANYMAWGQGEEPGALAAEATALIRNRRSARQSVRRRMVFDVEVNPAIGVALASDEEDMDPSRLRHSCAWSHNTTYVQSSRGDGEAKFLTLHEFRTPPLHVQPRSARGSFGVKIRGTAPESVGGHGTHDEVSPCSSDRAINGCLSSASEFSPTDMLAYRSGSDVRLGEGSDEQTLHPGSEDSAKRAQRAQTRIPSPAGGSQLASRAEDRRCGERHGKEGWGTGARHSYEGAASQALRSHEAIGVVQQWLEILRTQSAGLFISEAGSAAEVDTGRPVGALAAQADAPPSRPRQVPPDCKRGVVAELTGDIGTALQVLQYAVYQPLGCALLPLDPSTLFQYTRRFAETVFKLEIHLPEARDNSNSTMSCQREPRPPEPRAVGFTECAGSSGRRETEPSAMIXSRFRVFSVADQRGEPDWGPPGPAGNEEQAAGVLQNLAPRMRLHETALAVAGVGLSFQATDVPFRAATNRSEAGEGVEENLEGAAIEAAEETRSQPSWGNLQLLSEPTGRPRSSSALEIPRRREERREAPDERNRLARLSRWGPHSNNECRLERGQRVTGDSEGQALDSEFDAQSEQCLRGYESARAFARRGEARCGGSAPTLRCLVRLLSTLSACRRPRRVAVPLAGLNASAATRGLSVRLPSRSVFTFIGLSDAASSRRQRSGEAGVLLPSSSRWRLTAELCVTVASFSMRSEQTARDVLDVVFSAPESEGPLGYAAGEQEPLASQPSAVQLRSTQPGSAQLLECGEVAFGGEMRRRLRERLGASASEYAPGACYHEERFTLRMLLLGPGIDSWRVATGAAAPINRLREAILQEQAFGQPFMEEPSLELLSEARVEGLCVSPTVPEPGAADPGLAEQEREYGFEICATHSEDCEGPDGGDCTFAQPRQPRVSAASPPSAPPLSRSARPRDLIAQYVPGRLSGPADGWQTVLPSRASSSALPARAEPRHVRAARREFAMHPRAAGPRLTRALESSRQPEEASRNYHILGRGERRGRTAHSRVAMLSLAIHNIASQELKALDHLEESISVVPNRGRPDVFTADCSVFCLSGEAGAPQGQTRSRERQPPPVARDRQVAGPSEPTESMAHLWLKVGIELGTLRAARASRVAVYTDRQAAERPLGGGSDGGEGCLTKVSCEDGKELLRRTYQNDDDRFDNLWQSRPDITSARDSSSASGMALEQRSFRAARLWRLTLGFRRDGVEQRRRERAEGGRQFWQHIDRRGSACSRGFVREEHSKRCAHDGATTFTHAEDAMFSFEGKSEDQSLRGPVICFSERTGQEANTPAFEDQSLRTALFEGDPLLFDLSDPWPRMHPAVTSRFLNGAMRWERVEAPPMTHSVKWPINSEDDAEIETYRSFCKVKTVRWFRSDLRAVAEAWYFTAPESSRGLNSHRFSRQETDEPRRADVSSWCEKTSASQHETPQSSSDSLHSHMGSKGDQVIDEGLRSCMEFHSSLANRREGAHVLTKERTACEWETVKLPSLAAREQSRVCQFFSSAVGEPAEGAGDESLRNMTDLIKTNLFYRASKKSMSSGLLPTPDIEPRSSEFSSAALDVGEEHVRGLLGCAPFEPSPPAGKLLHVPCVEDLDLPASQVPRPHARVPGGPDSLRYVDARLSTVFSCEPGESEPPMSRVTFHELGAPGPYEHYMGSIRPGVVSGVPREAELATASTRRSLRMGITSGAASGPFAAHAYSPQARQTVIFRPRTFEDAQARTSQLIPRVRRALGAEDELGQEEALSRDAATIPVLLAFMDDKVMVMLLVGRYTCRNFGTDGALCTKTIGVVGYDYNEIPALSDTPDPLESTLASDGADCFAQLGGVSVLALRRAFCTKHKLRYAEPFGGQSEMESVDQDSGAAPYGLDESLADAFGTQVPADPLQGRLEPATPARGERRDRPSEQPTLAQQSGREKALDANAVPRPQDLALGSLWLIGGRVAEFVCSGYADNDSGVGLQQSDPPLLEWRDNRSASANGGPPYSFSADARYVPAYQYSRYLRLTLSPELRFHSQTTRRWLCSPELNTGHRMEDPATTAELRHARVDYRPHRRASYQLQALDRREVQGSFGDSKVAATKRKSVGSRRMGDSQESRQSRMCQRLEPCARRVKGLRELDRVDDDILASSTSQIADRYRTAEHSSGVPRCNDIFRRSSHPEPPRALTSFEEFMAVPGLRNGGEERPPYLASSCFRISLPCRDVRRDAPEPERNTAVAEVSAKACFAGAPQCPSPQAEPDAQSPRRRYSPMLNLESRPSRNKVYGGNGGSADAGTYTSGLSNSDAHALHGPLPESHILLQTSDEDLAARLRAKLAWRSCCRALKEEQLTCLAHQKERKEINHGFMGPDETNAAATARTARLFESLVRSELRLLHANLFEAPRNLSYNGRSGLFLGCCVNATVGIAMASPTALLGSDARLLRRDRVAGAGGALLSQFIYDLASIGVQSTDQGVPPGELCELLLSSARIGLASHNAKLSGSVSVVSANPGANPDSGFVGFYRIFRIRFRPRLPARRRDPPVETPGSESTDEGGAAQASLARLHQRQEHYESPNENDTDRRNFGASAAGHDTVTVSPSDRGRPRGRQTCRPLERTPRPYALFEELDQVTQPRSDSSSDALGLTSAIRFEAQGFMANLLPELERASDCELADTCFAYPGVTMLERAAEEALFRFGLTDRDKEKAWPRQFAGSEECELDVRTEYMAQSKQAQEQVRVCPKEKFRAHKLLFVEVASFEPADSELNRVAESGARKDVRDTIEPSGGDLTETSFLFAHNIGAAADFLQPALEPLSPPSAIHRLNPTEGAAWATAWGGEERPFLANEDDFCGRPGQSVPVVRAASPASRVSPVDPLTAEPASALPWEASHTHPSAQSAPASNGARSALVSLGGVRRSYVEEGENNLDEVGDPPLAPLEGDHHVLQTGLGDAPVFYAGWSSVGTRCVSPIQATSRWVIVEEEATSGRSLSTKTEQIVTSRMQAQPGARASGPPLVPATIAGYGESNRGGASTGGLCGPSELYEGDGNEELSEEELGSVDTETLGWTPRNKYDLLETKGQADSENAREPEQHRPPENTGAEYTYAPGPSVHPVPTAEPFPTESPTPLTTPDPCLPPGRHLPRAAGDALRESDAILRCSSEKALWRFGGSRVAAGVPSARADARPSTTAAAKPSGERRDFKTLFIGIGSIRDVPDVQSQRKKGRDGAERPQPYQPSEERSEYLLSGHTGGSDRLSSKPETEEGVGLAPEMANKDVASSHSIAAGVQARQRILSTGQISLAGVEDLLFACIAGDKRLRRAQCSESQWAEHEVSLAGDLDSLSRRPRDARRRLSKRGPPYIAITAAGNHWVRASEFAVDMSYGFDRLERTLHQNALETAQCRKEAKDVQAPAELPQMDPRLGAELTVRDDRPQAHGASNPSIPGSVLTVENCPTNGPSAPYEEGGLSEGGAQPCSVEESSCTIATESATTPEVPSNEAWNAPVGMTAVLAEMAVLEAELAGREAGLDPYEPDAPPEVGEPLAPTGILTFGQFTLREVFCPVTGADGLLGTLNRGARLGDQEAVDSKTPKSRKNKCLAPSISSNPDHARERRRMSAVSAAEAAAMGNRRDCRTELTTEFGQVVSGRREQHAASPKREARDPTTGPPADVDSLNPEDFVSLVRATTFNFSNLLRRNFPRPLQARFDKYRASLPVRAVTSGIEGEPPGTFEERRRPVYDGDTEAEFRGDRPPLSSFGGLGDPDGRARRGPTGGRLFEERNAPTGPLRCALPSHDSPPRWLPPTQWAVNGSAHITTEAPGLNTSRATARRIPQVPADRGQFLRDAQPAALHNYGGVLPGLEPGSKFADRADRKELLYEAAYVEESAQSNFAARTALAHKSMLLSLKPPAWVELRAAPADLARAGWTSSPLFAVGATGMPQLEVALVLPAFVRPTKPSLPDRALGVCREGAVGTCFEIGAGVPPSISSIIQIIRGVMAHDRERSRRSRAEAAFCAQKKKQLEAAEACRRLLNLLDFQAEQGPSDEATRRLACEAGEDEMECRFLRLPQICNSEAHDQYIEHDCLDPCRRRAGGLSAQRPGIEQRIRDAPALESDFPPPEVANTTSLPSYEINPVDVMEYFWDDYPEERRSPLTRSRAQFSLGSPYPGASGSAELELVLGVPASGTSRIGRGPRHICSSRLRGQSAYLERAWSFSVPAPSDPESQDGELLGNDRMQSLYVASSVPGLHVLSKIVASESDKLNSPKQDALGPHARDCDPHGSVVAGQAKRSVLNKNPRYLFCLEHRGPDVEHAAVRSTDVRAREMRINNRFTTLAFRVRFGSTAKRCDRCAPATVGYEAENAGLLLQSALFRAAVDDIRIETCLADEPGRRMPLPLPRRRLDANPVQTTGLSAGGVISGALASAGISMLAGIEFVLVSGARRNLREALHPLPRFHKLTQGRVSIETQACLAVADGDARYACLGDFEFVLLVSGFTRSALVGGGHPGLRAAIYFVYTGTPGTPRAEVVPIRTIAQGELDVEDGVGRKALRSGREPRVRHSVRESHEPDRFAFGGDGPGYSLFKGYARWLVSLNVVNDAALEKHGVANSISGRRPRPEPEFSSRNAAGMAVFKSRRKTLAERERDLVGYVFNDDLRRGEETAYLTLESSEEVLVYEANPAAPPHPMDIPAPACEGSGRTIGWEDTAAQACVKRGPGPSLLTRATEIPSGPSPAAPSELYQGEGRFTCFTETHEEASGLAVDAQSPESMRIPELLSVGAVTRQLLYAPNKFPPECPVMLTDHAFADAASAEAVAACWEVIRSPSNPPTDPTPPLHADECLPFSGHAGSWEDRSRQGPVDVPEMLALLSTCRREVLYDSLEALDRGARGPISFAEGASFLSGREVRQRRWNPGAGVDFRSVARAILFRRKRRRPKEIDPGTLANYPVGAETEGLEESRMDNFADAMRREAVTRSELSYWMKNRYHSLRPSRVADAKEAPGISLLGNRCSGLAEISQLQLTELWDVAVAVGRGASRDAFLGQAEEHLLATLNVTSTQSLAHLFSEVPSVAPVPCLVLAEAIHCPEPALSRRRLPGELSDRSYLQLLTPRSSFLSADTRPGFIRGSTRALRQTSEFRNRQGAALNLFPGLSSFQGLSSTQARRRLLVSGWDIPSPSGGAPASPSPPALLCGELENQVALPQKPRIYPQPPHDEATATMIACYQGSTLRAPAISEIGQYRLIDSKEVKHRAEPARRYNSEDPGAGFIRLDLDAQGALAAGSDNPGVEQFTDRVLECACPSNYADYPSALAKVKRRETCRGEGPTVLPDQRLPTLVVGEPHGGGPILTRSDAPEPFEAPEYMRTLEKPVSHAYKYQQVAASGYRRIQDLDLKIADTKAEYGASLQESQVPVSRYTKEAGVKDSLSPEIALQVSDTRSVQAKPSSSPFPDNSDGAGMSSSKPNKAEGKTRLEDKFEVSGPLFGPVLKSASAEVEFHPVPTFARRKESERAPRVERQYRPLRVSQLSLRRAEDRLDGMFFLRQIKSTKRPFAESGPEAAHRKRRNFARVEPEESASVYAALLLAASATWKSALGDCAERLWTVLEKASRAQRKGALTFRRNHEGSSFQNRISAGSEAEPFWVIDEPLPACHYPFAPVEDSPLCAVCFSVVFPTPQFLLPSSLRDPTARLTPSEVLENPPAFAHGPDFHAPSAPSSDGEKVYDDDELVTDEVHPHELLTLSEMTRRRLGMGIEMREESANVEGGRARLAASFWSGCAVRYDTLVRRSSLSLLLSSRTGKRGLTAGRRRMPGDPDATGRHSRGAILPGCIAEVHTEEQWPRRSYTTEGQLPRGAAQYRYCGLGKGDQFEEPRRMVTDRENVEVLFEAARESPTRGHAFTADANLSESSCVSEDTLAATQLMSNSTCRPNPSPLSIFGGAMPFSANATQLRYLVGLPSDALCLVSKADHGRFKERALGCAVSGSIGLPLPMRVLCGDGEGQDTEDDQRDRAEWDRLAEAARFLSGQVNGAEEGVPFSAVPVIFAGGPSSSCSRAASWAESARRQVEIAGVPCAAGARSSPSYLRKKRGAPSTLEHVGRDGMPRVDRVLMGTADILADFDPAGLCARAWRPCGSSSAPQLDDPLRAGSARLAPISAPHRRPCKPREHFRPQAPEGASKGVREAQAARGEVSPRLLPEAPSVTNPRERVDPIRGEELDSQSLGEDGPLLTRNPVGAGVPTVRRPERGSSGMISRQVSGLTSNEKSGTATSAGCLWERSAPVSLRRQTASKTRFVCSDFMLHLMKLVHGTEEAEAEPIEAGGDAFRAARLSIAFSEVLVDASGVLVVEEASRAEVVRVAGSINIMAGILCWLKRGVATALVLGHLHSERNEVLKDLVDRLGPRLPPLRAARMRSGLDFTISKFRSGRVNALAFGKLSGFGVGDDLPISGASIPDSRRREYTASPGPTELRVMEGWGLEGHALNKVEVLSIRVADVGQAAALSALVYSVGPTEPPLPPEGSAPIREFLGFLRFEWKPVKVKGAQERLGLSRDSLGGLQLTQVPTPSKAVKSLDFRKKRACDSTRRRLSNSEIDASSTQPVEDPSKCMSKKQKRDVPRRDSVEDGWAGSPQDNTADSPLVEAHSHKATALMLSIVAQPGLTQVLVRDRVSGTTRVGMTVTVSIRSSNDSEASRPAAPLRRPLWQRTLDSLDSALGGRAFPPPHADGRDEEAGQTARAVRAEERLADPRRRSDSSQPGQIFSLGAGSTSQIRLLQGSRAEDDYGAQCPAWWATEGTIPRDLPAELASRDSGDHYISEGTLRSAGGSVILVSLTFEEQISGEFACATLRAVPCAMAQEAEQFLLGVEYLRATPSPSANDLRMLERTGQAGNTQQAGVPDTHSFNQLAASYAAWFVQPFELGAGGESAREVWNYEDKPEAQYVQGVRTLPLVPEAIWLETDDAGLVRAAIEMDSGSAAALNNRIGWIDEEPRTPEGTLDARIALPACCLELANASVLQASADEAFHFPGILTAAMVLDERPPGLVRSATVQQEPDLEFEGTHGGATSGSWGQALSNLNNGSTFGSADLRLARSPSRPTTEGSRFTAAVESNRPAARRRSVTSRLESRRECFRLLLMLTFSSCRETVRRSGVVSEALFTFADTQVRLAASGDRTQSRRYRNGRFRSSLASTPRMLVSSESAGGSVVALGLELWSPEADATPAVCAHASEGIPALEAHSGTRAAAETQLHEFSGLRHAPPTIRPTAATRESPSSFCRPSGQRGLHACAISSALDRSARDPSGAEMREDGQAGGANVITRRRFPRARGALLVQGEVEPSRGHVFAYPSSRALGSAAEAEQACRLSAEHVCFYIRLLALEQRPLEASPTTDVDQVLLREVLVQHRERRQSSYTEVARGTLAAGNGRIPEGLPTGFAHRSMRAGVTVPSASLRMDRVRPLPPCERRNRLETQTERCFYNEYAARERELRCEFLSPSLTADAEMWRSCSSSSTARAHHRTMLTESPPPSFGASFHTGCAGQSQGEGDTLSGFSAAFHAQMAETIALVIRPELRPGAGTLGARTEADPRVRLSRFIGRRRRIAPRPREQGGADLNAGTEEPPTLREVTMLSSTLQITEHLRQSSADGAQDEELESEVNAGQQADSVPQALLGRASTWATALNRSSDLLRSAEXGRADEVNSVEVGQPPYDALREGRNLPNLAPPLARSPIQDSIFCFTERIEGPTDRLVTSLMEETDKALETDWGSPVCETPDLGLSGEAAEFRAQGRRGRSSRPMRRRRGRKARQRETRENLTLKMASGNGSQGETLEDSAEEAGGHAYDLESKVGSVGASESVDRIALSTLEVFVEMPRTVAARHRPNPRNCVSEERAEAVKGHQILTNEAFTSAGGSAGAPAFLAQDYDGARVTADLESPASLQDSRKNRGAAESKELDLAPVCSADIPGKFAAWLRTSAQTCLDALRELGERSLKASEKNAREAARTSQSESWSVLRSSQRAPGCATTAPGIIELERDLSPGLYPLVVVADPAPEGRALVCPLDEQASRALACMIEESARFGREPRLRRCSTLRRKDVYMETLMRRRVPRLMSAVESLSTKFVVVLMYQETAAFGVGAEKLRRHTDAGDVDADSRAKKPEGGPGKARENRRIVNPSASGPEVTYRLRLAAWLTGVSDGSRCREPTEEVRRLPLSLVAQLAVNQRLPRSKCASTSEVTVEMSDCVRLDLPDEPGLAPSLLRAGFDSWRGRRPAADVSELAADLSGNDAQEGRGPLPTPQRPRAHLHWVSPGRRVADYDQSESAYYARFTNYILIRQIKELRRTLKRDQAPDHLDRGWDKAGLRIPSGREPEARLLRNYRSTSQATLKTRLSGALLEKRVANFKTFKPAACGKSSEPPHFDGSSRGLFEPAYSTMNPMQSASSALSARVSDRLIANAGSGVAYAATGPAAGLSPNGSLIESPDQRLAGACELAPASTNHIEQTGMRSPRETKQTKTAVAESASHKARADFGAYSAAIVCTGGHLRGSLTSARLRAGQITAMSVEGSGDNKMRLLLRKQKVGVDAAAREASPELRPSSPAHPAFDGCAHPRDPHVDRRRMADILRRGVFFEKKCRFRWVRPAWKSANSVFRRPAQDGLRKGCKPVGRKYEEFESIARSSRLHDRNPKAQRARAPSEASDRTSTVGATPGPRRSRRYARARDLADLLRSADESETILAVLLPDALRSPLRGPSCSVPGGVFISMGRFEAAAPLGLSRPREVLCGAAFALYRSISVTDYPVREPAAPPPPGAPVVALQAHGLLPGEPFGVQFRSTRAAAIYESPGQGKIDCDARLQSERIHPSTCASATHDLDNMQGVLLMGEFFVSNPPPGPDVQRFRRPASETPRQSNYRRPTFSHKYQRPGDAHVTSQSFEHGAMPTGISARLAVGVCERSAPQHKKFDLTDATAEALCGGVDADIESREIEVSRRDHQARDEFVSHERLLFEQEAQPLDRVQASNTGLKDMATGCKHSRFPCLFKVGVQDSSSLNVGQGVLENPLASEPLTGQEQGTDGSPGSRVKDESALSHEARQTDQLLPTADASVSAGVCQDSDGQSDAFFSGRDILVRQVADQLNSVYESRTRRDPGRESVAQKQVPRFEEFGNSASEAATPIRRKFAKRFHTLKYPEKLRFRSVCLRAAALGQRVEMRLPETRPQSEIVPADLQDSAVIFCYTAESFEGPITTEIAALPFSCAERCVRESRTRSFEPREEEEALVVAEVQFSQFIAKNGEGSWGPSVGQDDPGQAASRWASAAHDRGQEALWLHGQSAHADESQSVSPLSSALFAPEALRGWIQDSRWRPGAARASDEWAQAVLKACAQGIRRRETSGTNDDGIGQLLFESTFVFYEALGGEDRSQCREASRVDGRDLAVACDSTDARGHEPAIPAVTVAACCALRTRARGAANTRGDAAEASDVELAFGTQSVSGSRSLADGGDLARTDRHHRDCESAGAQSVDELTGAIAPLNAISEAVTGTRCEQASGLELSSTTADSRSPTLLPAVIYGCVRARTVSQGVNSLRFALGDYVELRARNIFRRRLDLRHTKEIGQHGSPGARLEAVENLNHSRPQPVSAGRAWGNSYPVPSEALCWAMAPRTSSYGADQPGAPTPGLAHAGSFARGEEQLPIESGASYRLRARRLRRAPNHVTRPDRGFNPRPRNPDLTWRGAACEGQEQNVGLLAAEKGGEPAASSFSWSSINRVPARPFERYLRKSGTGMGLASGGRPASTRRRSSKRRTVILGVFGGRCSSEASLLTDRFSRRQKGHPCKEESSRRRGERASKCSGAATVQIDPETAFGRGSMQREGRESQSRPSLAWRDFGSPSDFDSSTEHAQLFARPVGTPNADPGGRGTDGASPLHHVSPYGPSPDPFQTELVDFAAEAPCLSPAAMDHPWWQLRLATLLAQREHTSLTIMRTREQRSLSASEMRSLTTFVRVVASRIPGPVLAEILSPPRTRVGFRLANHDEAPDGFQRRRVRFLLSGSACAADQRAQRSVEIDAEIDALSGLSCITHSTRPMSQVLKPRRRIGFRSGSSDIPVQEAGDAKSNLFNANRAALVFGEVCSPFPTPEPHCHRDTTLASPIAMTRSGRDAAEFTGKWGSPKPREASHVMSKPRKKRRRRELEAFRGLGLISEELSQFPGVADAEERLGEQDAIVGPLARESGGGRVFLAICLIRCGVTPEGDGWPTILAEGDLGGNQFARSKHCRLPEMESRWGRMVRTANKVRCFRSLRHFGEVSTCLLEDPEECEQLGEIDQELGSTLEGSPTQGPAILGTQKRGDSLLPSLHDPPRLAPFRCRRGRLSSRRGGTSFPTMSQVAFFLAERFPLEVLDDPSLGMVTEVPLPSWAVRRDPDAWESPSADVFSVQSEERAVPPSSARHNADSSPVYYFQLPSIPSRSQPYSVFLQVLPLSPVRWEEPDSLFPQDEGRVLQSGAESTQPISEGSAGTGAVDASRALRECQRVSGPEIASLDAEGLRFRGDELAYSEFMSNLQRLPRQALTTVLGSQLEFSGDLSFALLTLFYFEPLQEFPPRPRPVRPVGGLGHPPTFAFHGVAAGEVEQVAKASHSSATANLLNRAADRRRHFSLGRLGHRSTLFRSAAAKQERYPRHDPSRAGRFVAPCEPRERAPAEDESSSDDPLVSMARRHCPPRSVVVSGVDREERNSPSWPGAPLGMDLDGGGPVSFVSIRPQFVTQGSLCPEFRASVPSLPIVQTEPDLNGPPPACLLEDPPELTTLLGEGRDGQILARDALYSWMRNIRSGPSLLDQPDEDWPAPSPFDAFGVPPTYDPALLADLVGGEGHTGSELKELVASQKSADWQRFALNLHPGSSQNPFAMTFEGDVDREITVRDSERQRDAQTAEGQDKRRAAGYVPDAQQLRLSSTERSRVRTPGPSFESVYSIVTDLGNFQFGAGESGRKARAEPTGSRVLSRSGGEAFRGSPGDTLIILSNSIPALLAQRKSHAPSSERITSKRRCVERIRKDEAVSSPADRGPLESPLAALTGVGVSARVSSFWGAVVAGAAGRITTQARSQAVRPTGSAAQCSTPSAGIYEPIQHVRDGLFSLGSEEFSCTDRYLRRRVALRPAELRSCEEEAASVPRAFRSAPQEDVGPLSSGPPNDGAAFRLSVTELAEREALVRVREQLPTQYDGPGAAEGYGLQSAGGIPTKDAGNSWFPSTHPALVGATAPASAFGSEEDSTPDTSGHSYVEGEGRRGLIGKRFSSEEVHCTRSPPRDVLAPLLPVDSMRPMIGPSEHPGSHRTVVRCARRRSSLRDLESPRAGSFSGARQSPSGLVSQAGDAESRSTESTLAVVQTFRSTGLAVECTRAGMALSRVAAQCEAGMTKEDPPYGLSPSWVFARAAHGNLVSSVRLTLFSPWDEGSSVSAEAVPTLYVPEGFVQSADRPRFALLFRMRMPAPSWLRVHPTEELLPPLPAIPISGIAQEGSMNENELSAGNPVSLPGGGGPDQVPPDPGQPSHPLAEVWRPRLRVSDKYRDRVGYAMSMEIGLAANRGLGESISEAFPAGPVAECKRYQREKATTSESVACAEKNPDGRLHVHAADDTKAYRPALVDRGAAVSTVDATIWFAPSQGLPSGMRRYRVAEKGASGSLGANGSDLRPMEATQRAPPDESHIPSSSHTSEITVAWESGKRVMDRTAKSVGADQGQRCLEYDVVIRRLLGDASQVRPSPTVESEPSPGEGRAAPANPWCVPGRARNENSGTLNDGSQQAEPHPGGNLRMPDPPFPRWAARRQSAAPFPNDGPPGVGARSHERSRATAFENGQRGQLQEGGLTHIASSPAITARRNGISAPASWVMHQAFPLAYALTSMISITLPSIALTSDRSRVSRRRLRANRSEPDACSEQEVPSIDVSGIERRFRRGHEVLSAERLGEDIAVRRRDSVVLLVSEQSSSSEGPAVSASNSTSVTSHVPSRASRANLLGSRRLVEAERAESGGPSAKTSGDGAHVHDERTLSTEDLRVTEAPGSTSEGPSEVLRAGRVSQRAATELVWFGEHLNTLPRTGTERADALRAGTLFQERIVLKEWPVAVPQLSSTPLAPRQLSHMGMSLRESAETEDLQPLNQDLPCIALEIPQFESTGDCFEAAIASRERDVRQLYAAIKREEPKALEKRPQPSSAAFRMLGYFRIFDFSMSLADADDAVRETPLFRVWLQETPPDQFPEGTGPPPGNRTESSTDQHDAGHDADSGLPVPRRTDGSAQALGGAGRRTRIQHVFGAPVTPSCPEVAGPQTAFLSNCSSASGLGEAKLPPRDARGYADGARRSAIADGAEDPLQHARESEAPANASYGPSGPEPPWCGRLESQALANTRTAPPEEIWPPYARGSPAPCLSRFPAPPELSPRNEQAILSQLTLPAEDVVFEGFPGLLTTPRMNDSTMLHGRACEAEAAARPDESHLRECNFESPSGKAHLQCEAMEAGAVSEEWFTSSGWLSCEALLPGQFGDRQEHIDAARRHRGESCSGIETPIAILHDRTGASDACRFLSARADATLAPVLQGRTGPVEGLERLHGELGFHSRRCVGQTRGNAATPMRTDEVLSQGPCRALGPEVLTIADEELVTADRSFRMRRVRTSPGRPELLRGRLPCSEKQLLLRRSTLVQPWPLMWGGRALSDVRGSVRSSTGSGPPRGEEAASTSVEFAESFALSGGMAPRRVGDATSAAARRRNRRAGSERTLETMRREFLRDQLQEASLTRGKVSPVGVRVHVRCIKLAQVELLTPGWSRARDEALLVAIGSAFGSEHSESDFEVPPFSAESTDGPECAIGFALDSEDDPAAICVRAAAQGRSCRQAKRGGEYIVGLPRSAEREGCRHTSPCEGRDCKPLAELSYLNEKESVAQENLSVKLWVVFTRDQFFFPEEKLTPTVSASLLIRQEGPVPYPRGVLDNAQPSFLSTQGLLTKESAMPLPTRVGRSARGGGLFPVSSSEAEQEPRGARMEHAEKQRERQRPVRAESRYSRLAGGARRSAKDDWRIGRETKLNSTAELESESPSPATLPLSDANFLEATVGEQAATFRRSQRRPDTSNSGFGLPLFRDGLRRLSGASRYAVDKRDSGEHRYEDDPMFRSGGTGTIGCTHGRKFNSEKKGTAKFRRSQGLWQRANRDVLLNLFTLQTDPPPSAGVGPRPVPEGLPLPAIVGSEGSRLAPRLVPEELQAEARLLAVFDLHGSGGSRSTGGKPASLHPTARGLLSSFDDDLRLAAVPVPDGRPDFAGQARRRCGTSSMPSSMPQPSGVPHVTVRFPGFLADARLSSIGQVAAVNPMHSDIRRRLQRSDLASPFSRNPRTDSGRKEPESSDRNSRLLFMDVIRARRELEAEAETTAAESPHGLADSAAQAHLVGVCETAEPETGVPRRTQSEVAPCTVQFIPALSNAQYTAEEDLAVCTPPAAGLRGPARLHGELHVGRQRLLHGHEDRAWECFGRALALRFLERYYSPFLHMDNLIGSFSGHHSHIAAAGWNISVSLIYAYDWGRGRRRRRGPSALCCGHALSRNIDKQPESEGQPISPGSQLGARVTTRLERNETGPGLVLLGARNAANDGVKATVSVQQAVLRHLFYARRTGARTELKTHVFLVDDRNLRQPDTLTLAETFMEDESIFPALGPTSAVSVSLFLLTAFGLDVRHSGRSLPAFPPADHRPPQRSDPGSGTGSLSSSTSASAANERLGHPVVTAADFASLDPGLTADRLSTYASGPLNPPVTAPSSLMEPPFSILMNETISAPAAFPRDARFPELVLEPSSGRAEIAAAYSFAWRSVSAMSNERLFEGTAGDPTEVAPAGALPVEMDATTRSRSHDEAPGLDPFREAVARKRHLSKWVKSAQRDFRARYPELSSERYGVTRQLVGFAPVPTSTTEGVSACWSKSLELGRFPKEQPHVRPSPPLEGPEFHADGAPNAVINVGVGQRAEEQIETPRPNRRKPQELSAADSLRGPPTEFGRNPTASADVESNPDRVEVDDVTMGTDLANPQSPQGTVQGLPDVAPGQAGAPPVQTTIPLDPGFLDRPIVQESDPVEWSRAHPSCHVELSVPSAPLGGTGADSEEVARLAKVDGRRSLARGRAARVTLTRYRRHRAEHGLLEALDSVVAWRSRRRFEAGARSNNELGLYAAEDNTTGLERRRRGPSSGVPGGQSLRSADVWNETPWLSLPEAVGSAQCPPRWRSIGALGCPRVAIGPDSTDNVCLQGTTTFPLLRWDRGGEEVVNFSVLIPEPASGPGAGSLNSAPSSFELLHYHACARSLRASSSLQSVFLSDAAEFPRWLSPLGRAASYPHEDRLRNELFASAPYAELPPLLSPAMDFMQAILAEERLVLACGDGLDDEEGNATQYPDAPPAADDVLWQDAVTGGDRQAGEEVFEFHSEANGLCTATLGRFVSKRAFAMCRRKRVRLSRSGGARMSHIRTREARNPVELDPEELAGLVETRAHGLFDNWAAEVLGRARLVGPHTFRLVPRRVRARASAILQEERVLLMASPGLHNEALWLLEFDCYNLMLRPLVPGGVPVRASGARAWAVSLRAGLIADTDSLRFASRAGHAFIMARLREPSPRTEQLNGPPVIDEFGLPQTEEPAQTYPLNSQEDMLAGDLDSRMSAARVAWRRQIDSRDTTRLSPPLFATTRQGSLERSRDLDLLLAAFAALAPYSPAAPPPQPILLEARDEHVAQLVPSASYRQGSNVRVASLSTGEAVTREQRMVEPLSFAFIPYLDGALHSLERDARCFKGPAHQGRDRHGYLLRRYPPVEGRARCGVQRSARDSDLHTAEGSRELSEAILIRFSEEDVPGENRYRPPQWAAASRSLPYIDETLPVTAGAPDAQLVRFALDIRNKEAEEITEEKTMEFPIEKLSVVRTLECARQQHLRGWTLRSPQAANANRSPARPRQTMLQLDESAPLGPCLRVPYLSVSQPAFVGQSFLSRSGSAQLPRSEFTCVAQHACQRDENPHLIDTWFHNRAAVANAGTRLLGLLTGGQLTHLPAPEEAAGEAEEDDQTSRSITRDADGESPAYLQQASSLQSEDYPAGSSPLDRFVNQANFAPEGLGVGLAAPGQSRHPVVGRSSKHQAMMSAKCQAAGFTEKAIARFRSQMDGVRSVHVNTESLPAAGDGIFFAEFCASAKSGDLAPLGRSSSTWIRETATTHPRAREAMVGGINEESPLAAAWGPEIGASPDGYVSFGEGTGEARDSENRSYEDGVAHSRCQIGTQRLSSFTAVATEGTVNPAQNESPGSAADERTLPTAAPEPVNPSVPESDETYPVLSGLESLAHDDFGASNEVLLPMAAGDACNHFRRRELPVLDQAHATLLSRASDSGPFRRLRDRGRDGARLSGATFVRLDRVDVRICLLVVWLEEAALNAYRVEGTFEDSVSPAVTLSVPDGTKELAASCPSYVVFQQDDADEAKAAKLVALSEAGLSRRRAFPAAATRTKRDESEEGTNGSVNVSGEQCREGCEREKVALGWLLHEQAGHSLSSEREEEASEAAFRSPESSDLFAFAGLTLEGSKSLTLEDMQSLLTNESEAELPSPDFQDEGHAVAEREHAHCWSMAELGCGGREGKMEADDDTGRLRQAAAAMLWESAYGAKKEKTCQSRGGSQRARAPRSLLVSNPATHPEKELDGTLRVYELGQQQGGGLRAELAVNELLVEDRGPDNSNYVVAVKFPKAGAKECSRKKDKLDLHGSCDICAGMGTATSMSCTYA</Seq>
  ...
</cvParam>

<userParam name="D:/Software/Databases/Neospora_3rndTryp/Neo_rndTryp_3times.fasta"/>