Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_19004.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_19002.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_19000.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_22048.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_19003.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_18990.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_18991.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_18989.xml.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_19002.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_19000.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_19004.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_19003.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_18989.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_18990.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_22048.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_18991.pride.mgf.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_18989.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_18991.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_19003.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_19000.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_22048.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_19002.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_18990.pride.mztab.gzftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/06/PRD000544/PRIDE_Exp_Complete_Ac_19004.pride.mztab.gzprimaryOK200004310James WrightMass SpectrometryBottom-up proteomicsMatrix Science Mascot 2.3.02Proteome Discoverer 1.2Not availablehttp://www.ebi.ac.uk/pride/archive/projects/PRD000544Not availablePrideNot availableiodoacetamide - site Cmonohydroxylated residuedeamidated residueacetylated residueNot availableProteomicsLTQ Orbitrapinstrument modelPRIDEHomo Sapiens (human)Escherichia ColiEscherichia Coli (strain K12)22493177 Wright JC, Collins MO, Yu L, Käll L, Brosch M, Choudhary JS; Enhanced peptide identification by electron transfer dissociation using an improved Mascot Percolator., Mol Cell Proteomics, 2012 Aug, 11, 8, 478-91, 10.1074/mcp.O111.014522jw13@sanger.ac.ukFunctional Proteomics, Institute Cancer Research&Proteomic Mass Spectrometry, Wellcome Trust Sanger InstituteUnited KingdomPeptide identification using tandem mass spectrometry is a core technology in proteomics. Latest generations of mass spectrometry instruments enable the use of electron transfer dissociation (ETD) to complement collision induced dissociation (CID) for peptide fragmentation. However, a critical limitation to the use of ETD has been optimal database search software. Percolator is a post-search algorithm, which uses semi-supervised machine learning to improve the rate of peptide spectrum identifications (PSMs) together with providing reliable significance measures. We have previously interfaced the Mascot search engine with Percolator and demonstrated sensitivity and specificity benefits with CID data. Here, we report recent developments in the Mascot Percolator V2.0 software including an improved feature calculator and support for a wider range of ion series. The updated software is applied to the analysis of several CID and ETD fragmented peptide data sets. This version of Mascot Percolator increases the number of CID PSMs by up to 80% and ETD PSMs by up to 60% at a 0.01 q-value (1% false discovery rate) threshold over a standard Mascot search, notably recovering PSMs from high charge state precursor ions. The greatly increased number of PSMs and peptide coverage afforded by Mascot Percolator has enabled a fuller assessment of CID/ETD complementarity to be performed. Using a data set of CID and ETcaD spectral pairs, we find that at a 1% false discovery rate, the overlap in peptide identifications by CID and ETD is 83%, which is significantly higher than that obtained using either stand-alone Mascot (69%) or OMSSA (39%). We conclude that Mascot Percolator is a highly sensitive and accurate post-search algorithm for peptide identification and allows direct comparison of peptide identifications using multiple alternative fragmentation techniques.Enhanced peptide identification by electron transfer dissociation using an improved Mascot Percolator.Wright James C JC, Collins Mark O MO, Yu Lu L, Käll Lukas L, Brosch Markus M, Choudhary Jyoti S JSNot Available, Unavailable.Lccp, polypeptide, peptide, mKIAA0989, Polypeptides, ClvPrd, peptido, peptides, AW549739, Peptid, peptidos, ETD, Polypeptide, MASCOT, Peptide, C79691.Not Available, Unavailable.l(4)17, Ce, l(4)13, Gli, Ci, determination, Cid[Mel], Ci[D], cenH3, combined T cell and B cell immunodeficiency, combined T and B cell immunodeficiency, CENP-A, collisionally activated dissociation, CID, ciD, Cid, CENP-C, CenpA, l(4)102ABc, CAD, ci[D], Ci155, ci-D, Siah, cenpA, CenH3[Cid], CG13329, CenH3[CID], BcDNA:RE21270, DmelCG2125, ci155, CenH3, Ci/Gli, Ci/GLI, CenH3/CID, CENP-A/Cid, CENP-A/CID, CENPA, DmelCG13329, chemical analysis., congenital combined immunodeficiency, X-linked combined immunodeficiency, CI, Cenp-A, CG2125, assay, CenpA/CID, Ci-155, CiD, combined immunodeficiency, CID/CENP-Al(4)17, l(4)13, having extra physical parts, Gli, ion, Tandem, determination, Peptidomics, AW549739, False, fractured, Cid[Mel], Ci[D], nucleocapsid, number, Semi-supervised Learning, Spectrum Analyses, combined T cell and B cell immunodeficiency, Computer, precursor, Mass Spectrometry Mass Spectrometry, combined T and B cell immunodeficiency, Supervised Machine, CENP-A, CENP-C, peptide, CenpA, Polypeptides, l(4)102ABc, ClvPrd, peptido, has increased number of, sensitive, Mass, Software Engineering, Analysis, Siah, sensitivity, Computer Program, Mass Spectroscopy, Application, C79691, Mass Spectrum Analysis, CenH3[Cid], CG13329, CenH3[CID], Open Source Softwares, Search Engines, proportion, BcDNA:RE21270, F, peptides, Analyses, MS2, Software Application, Machine Learning, iones, increased number of, Open, DmelCG13329, Open Source Software, Computer Programs and Programming, Mass Spectrometry, number of, having supernumerary physical parts, ions, Computer Software Application, Lccp, X-linked combined immunodeficiency, allergic reaction, mKIAA0989, CI, Tools, Inductive Machine, has or lacks parts of type, Cenp-A, CG2125, Sensitivity, peptidos, Inductive Machine Learning, ETD, hypersensitivity reaction, Inductive, has extra parts of, z, Active Machine Learning, CiD, combined immunodeficiency, ratio, Applications Software, Ce, Open Source, data, Ci, Computer Software, Data Set, Arts, Learning, Learning from Labeled Data, split, cenH3, Semi-supervised, Search, extra or missing physical or functional parts, Semi supervised Learning, Spectrum Analysis, Active Machine, fragmented, Peptide, collisionally activated dissociation, Source Softwares, Engine, CID, ciD, Cid, Software Tools, Tool, Programs, Spectroscopy, mereological quality, polypeptide, Program, Computer Applications, Software Tool, CAD, Ionen, ci[D], Ci155, Algorithm, Computer Applications Software, chemical analysis, Computer Applications Softwares, hemorrhaged, core, Active, ci-D, overlap, Softwares, Software, tandem MS, Mass Spectrum Analyses, Data Base, cenpA, parent ion, torn, Mass Spectrum, hypersensitivity, Industrial, Software Applications, hypersensitive, DmelCG2125, Industrial Arts, ci155, CenH3, Ci/Gli, Ci/GLI, CenH3/CID, CENP-A/Cid, CENP-A/CID, FDR adjusted p-value, MS/MS, CENPA, Source Software, cracked, Engineering, proportionality, Spectrometry, Specificity, rate, MASCOT, Mass Spectrometry-Mass Spectrometry, congenital combined immunodeficiency, Computer Programs, Applications, Machine Learning with a Teacher, Applications Softwares, precursor ion, Specificity and Sensitivity, Ion, Supervised, cardinality, hypersensitivity reaction disease, quotient, Peptid, Polypeptide, assay, CenpA/CID, Ci-155, Peptide., CID/CENP-A, Computer Software ApplicationsLccp, polypeptide, peptide, mKIAA0989, Polypeptides, ClvPrd, peptido, Algorithm., peptides, AW549739, Peptid, peptidos, ETD, Polypeptide, MASCOT, Peptide, C79691431trueEnhanced Peptide Identification by Electron Transfer Dissociation Using an Improved Mascot Percolator AlgorithmE.Coli Full Tryptic Digest CID Triplicate Analysis2013-06-272011-08-30PRD00054428065516460991804982953585111454224942024527872842188090368099330845811363336351524260119832758385NCBITaxon:128068888561896111430118726355557114526236493461364031952065126957274670738538836411354615821582310665688954762721123294422291180992323122586365458333460792519365914320597129386558195851149315242592637371250232NCBITaxon:1272111957748186614885843104300245135867221755437408169180454266834453058612668351498225058149636745855452811320814795641003923751463694204943320896420896344597413797912838440066793529367156759388036716052165994048321659721659545501315282693042165915627161696833218321729204277944762376454317203094980197525556978159509439843948840479NCBITaxon:2157525338551531051067439899037122857759515205968762262311210884555588845587077918178081736309431794571698936160488409859NCBITaxon:37162104782679401505907148364320421061320491381693630355543204663263331199456545351102541110321745921612928867641002642036945694101676341021076127735113165823925472793342814613584301417298174633457744491675476048932128735675684030191726518130194111929439367110411310239320255598632582788396591047593474951652998355256631758543980110243260866310245980875741755518320196447145268045796631367019083233115611415535510421932555217634981812359871069955529NCBITaxon:4751850298335476113615741465477180066556484337677299767982510216998238976484074137351155711089725482444474153NCBITaxon:5055789969844100036465349334147147493548019467512991143597412764731370863265478765698353221599838192011106775772710348198524794640986099586157187176685991915729513722117110129292107687834974198602028091488406334249234235152335985988655974649987039202111072943311711397215987419085037117082711708284182350241451139692931902197822474636046147123749402375939723287581722532566489050794526591972211915853101774208588596NCBITaxon:615750521028307989511051989972375059576131720002634196102641088878176179212190659407121906772275885815689964975151950587244NCBITaxon:22023717NCBITaxon:17036122019998570506174767927450627249159615333554184005246432136861505964878486662941786661347515363291018194301086731018510184NCBITaxon:1763573039635586331492862876705801321650851865368595105135553482260710185687294296110091416333NCBITaxon:619184023210007348824123363630710470058127187878645159812894555663577553470951451225786260704NCBITaxon:13356262607052607076584574054163677483167233150561007133705654195NCBITaxon:305550445791399878168119011928752829126806315327341478281055524NCBITaxon:9606135858469008111167815022830519302836728593008529005NCBITaxon:56938268830640179469915101184994352581515901448242838111394426041937047592723708281677285035158199011951953267386370249240536088385816224888175626158355837153337605726711935019980861193502167879108579137113712724071906503714759175712562745757270903113335503728142433747924910078711082NCBITaxon:96157243359463318586260799141262200298492670NCBITaxon:1263719281249212528303856838569591169266100658123756127504542666255151978837503600941293497905463224535247214012575151164990851515143899237453747445446415243235959202228870515805955365550881579327160293851578114978633892894535936479437NCBITaxon:6854412754225117159010901341673871589552101296610306129671585158451584937659393432715910022637673388990461423451287689591198332966467041464792936576164280341160221641331599280382803536909108917689462181214108034817939228788929502711313329528282944568617493468191126526997227321890382107601247190400727159736114311402064119810871355477436581424507229533796982042321242231291632180334708714537209164573321535815754699287770202060328114319338293550833291292211487252649997283035739087183087267271037908550717629970767892683704152140532941281607839563924654898227377596207322086595882735551693605330797255181135491597495350261159556143213840607258781414471509493349194963401614334728005936046316461046603815184547448500356709747751240174841855601335755547920427460769946881037620148871005941289093164354282688500712303831389464940838283594144242322197857742171598921409212205851157781154756929793244704749906604162103591905158114452749907312989913112273170187546991103589915NCBITaxon:37296103609833418710491130798133679531640729946710340157865826453033373306383011306413992530642363650591169654788546981121162034317103372994044586207340115357111952965261174553111471613386541313166343055213231201798360253237125523299351299385057316317642619794011513458445772678728623219334151346186208621160791392227983516811961255228149539322323116761757312108077213487999948861856962814084341033519963218496209913924882097115338209611533920953304393755699286266447NCBITaxon:2697049339862436941103121958832050920290610130685999758644864324995252972467411583438942786378942625673786391233435514199834931799868655405534352914865451471245466104298635712467915164135825763288401937334508771823803912903912952971974869317978911028688999513373105487712516321389850762554701193806256318865713034431121308516558658862238NCBITaxon:44664946454636493NCBITaxon:1107114280062421242883564913751415167845881087439145943854331116781077854314408043933452703134NCBITaxon:11082953469397738218993182269003512838714595311688533996695278695954186942003089544869724436620665639545300558623355180426430869220030228481242642815047514991051029910298471472414452386262903195418329025120895574974311700893062186441930615755841310165382352308056557722382359399463601066016236010439948399471797482544404237610212790568813377518236355721162296298176771870931281121478610502382451855796694654318632051824066728297441739449323512450128853183889198853191113782559103716473516601261557228331349390NCBITaxon:101142845031631297801985738595239693934323795602608712134639598427529595266437334323223544314275242243081433619593133456594327456029169963112223360520121697952528386972852904643680121870733474727901013234295603127816111921940818829760381812498856312203401884397331274414163910724358885872520493692955464803834369122432640817212419355955217493991281614055920425465519458228860918382727592127442340817019332982972275985955712744201274426235455552857943284139961660187625482964718761437868149024748011991509564818822972543176101214801541204551384738481882945190695150303416633603648498505693101510528353528352693735294512637534052066987418649729722405212585941097677451804812310061911079NCBITaxon:81341269432271027943447256848479291146387033384991722617561094616143512032581205136521850523525944732054942334937347386452700044664499175918915825803880433303766862448046120678112202604991080612461962902224619732063752299186705118670575090681219387911879471868023980071868015723072154514683574125814081861175715084769183885803290311608611388869152167786721271103683997844597247512951398704351262469692812397713333995103430481381781821981318826821080228156100547624112292657163295755350192222197911119686669381979121247124614854513283882813951080230294911040145954161934139036312041622110665890326446071121041170612744321085956210283169412831666943694559729949514106588827114113161879010105841330879478447517415080817053942065423174471270709964153292428141119466984114545869537932920101981264690410661145755139251923239232014081576401316973160621213392830312383911283128224260512803395228110108328252535315285128112853353153498257419481478753623142410135674295105242619145481NCBInr 2013051911506212945912928299633941346959753863121170519351626539002134398031309800697810369018853225660173654856615664162425103695118702348334824688221187056386321219690226186129925016468606885656512623217219565810102865606165606442838656717136041602358700349415048022160100298823578613252911187002157641809699756655666452467134887937965223926291613633666336721751117645406560103789059232146429314344870933114767468342808NCBITaxon:405592359093226465236526212633749821787074982163472565690569156925693872249821165448720569734507699300166690510894491089448NCBITaxon:2759661410NCBITaxon:49326535871556895207108944410005896550873228753513524812637300693039266595887251211776872687238724872965498727134976724223130554417725784541581419198822445446NCBITaxon:120661174673104105909882497473446899601677674468587529600NCBITaxon:581111822637082484119165578457845848402119443955307158059656636164034624136810893161001428099612NCBITaxon:548681NCBITaxon:58205464143945033077522836373791966272905815260096059606875944670875622708626659649604323259570509335483309029829387834810626756726756643061512793654319474483854492394704721191523191701610896154831396916928782757364078211293145707529835206189257771285024805270126283485418985487715877962730025156304125994952869646964396444911462472746128746011345069638526385263996563024097639245264110909467469416348112386935174635231NCBITaxon:565995576784119562330591736582257313269796990346134434636064404213451124951533043479096109760616194032257329246200966927294227294351338968583554767894314696891280175576009681118696167807811869414361833303811869817194759321718118691443906NCBITaxon:10298NCBITaxon:7771257118387271566338404330618596948364190802703847664568703257310568708618218678661833568851350NCBITaxon:7803906NCBITaxon:15029903164515169431297029820762115861218451210719307910944609137494400209285201319747078529507619212638546146663915383379NCBITaxon:10239NCBITaxon:714173613095705470448300641751585923890037159084128108406972282334575412NCBITaxon:1024528104NCBITaxon:10243392017481097797067135622583313618550992428670652779658334240906200492910263494951034809NCBITaxon:6312406741307670703766191009408707487613810804329032176023993592672947474376032768917812126719285321773846451772177437104905615348119922512153239576769014NCBITaxon:722715697472664709131704720269713032769785962859634114761309130813071263871212035332648373153214693383234114793981583701314131349376083334131183333570471114970396553972833321018418333121468745504510801874920026272415300910766203505411490280148517501303713444143983NCBITaxon:115523988139927435623593117928662623168390614404211945995677716032932853422NCBITaxon:57593450899981033657861853365835174574283162731215360242718316277135213519948875058NCBITaxon:1040731627524271550277916797181349130627415496755027802915954126443239291586600255702127211355886755123491612965879309452031241051519284343581539858015626981182590247149133167845609906902725602725612725633544228410133562634166392867572279017904NCBITaxon:579653745757405741112335235623785483555222210457751262161310915755969154293101364139622421392139018573232714896230741164027812881048961601067574458024025122968335294413936658140366576257634432206672400540296543NCBITaxon:1170928231772981843183443226224697657554992295757575928459355618270667143673344424035318492231121054211527639109697622611117957529818826331843192294381527640986661362652810442179626782531751327804267608565050176946996NCBITaxon:13131712507953389427955880119873251979596214114082241408223264561421971014122851867631854315207677376777421926129454458057041744726724042649329NCBITaxon:1773208893208895207559101176645531523166330200436745101161328426265872139269635889542301953188291581966558839194366534112336814498224911550554382641310337998666940068845421575353115104298315468911129859356253232273075660469136165105612149165238976336316812149159704126308213494091328881885513613NCBITaxon:1865381889083264241916073NCBITaxon:186536621017366041185650315750393765573111623427306855743680863772163157491529526689535862048867NCBITaxon:1388629623059597552840031972917616089942917030027310523110091100904054100926465322432327605683406217860610645391982159739757499802419947427577580422777919552491313662394073130014640766253204104411117086937451547922119856119857299204072NCBITaxon:5920165636713926767162481450134408440877111977810740162699412791314781967949679540814082380394528135340381659668872292612351786162432312432301359923561271087671797854096409797882103529305243277627912924911557484090978040924093447135120253163761629838633178313625388658569441554018133971741687097966287732396692029793628993156343019223447137634338722279548663436628233456433169173623125924858611093667421386388420493211354724847947314473116968111290255161398128481317333672214407721316931555778122152250255183610036NCBITaxon:11266NCBITaxon:439488113132318679448485145494137499010041715916922596345910659213334991065901249615334542NCBITaxon:66224327544271243274213401123901716571678496410289688333295491249668425282652158109434326521577160197127908571622562237NCBITaxon:103572702NCBITaxon:1035811948816543605076011415784435590NCBITaxon:1035917072127263480081859347834132234380222627626189036419694718252863495598396427119136452726212726232726241160719117718912389931214102460523121894840321182131426970494032480311318080304903141798130521248343111477874909323848143711315368891841368417494080498040593194342714918256136491154373413156713164163159403021009714629772823525675060189519295214505111524962748492496731460519518766260201153348580021538186256226912328013603275614231422275119030491102214505204932101755275914282664179906914174609111020594082511211143919042762167539131463977851866139077527142735071061981353008559292148691719825214511577281414448340732036962232834959NCBITaxon:11676122962116343423754513678303086784952371094679895580158023627224931770000-0001-6950-4328