PeptideAtlasapplication/xmlftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Streptococcus/PAe000285/PAe000285_442_searchdatabase_sequest.fastaftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Streptococcus/PAe000285/PAe000285_442_sequest.paramsftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Streptococcus/PAe000285/PAe000285_Search_Results_442_201104200929.propertiesftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Streptococcus/PAe000285/PAe000285_prot_442_201104200930.tar.gzftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Streptococcus/PAe000285/PAe000285_mzXML_201104200921.propertiesftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Streptococcus/PAe000285/PAe000285_READMEftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Streptococcus/PAe000285/PAe000285_mzXML_201104200921.tar.gzftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Streptococcus/PAe000285/PAe000285_Search_Results_442_201104200929.tar.gzftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Streptococcus/PAe000285/PAe000285_442_search.params.tar.gzftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Streptococcus/PAe000285/PAe000285_prot_442_201104200930.propertiesprimary200OKLange V, Malmstr�m JA, Didion J, King NL, Johansson BP, Sch�fer J, Rameseder J, Wong CH, Deutsch EW, Brusniak MY, B�hlmann P, Bj�rck L, Domon B, Aebersold RTPP'https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ManageTable.cgi?TABLE_NAME=AT_sample&sample_id=312'malmstroem@imsb.biol.ethz.chPeptideAtlasProteomicsLTQStreptococcus PyogenesIn many studies, particularly in the field of systems biology, it is essential that identical protein sets are precisely quantified in multiple samples such as those representing differentially perturbed cell states. The high degree of reproducibility required for such experiments has not been achieved by classical mass spectrometry-based proteomics methods. In this study we describe the implementation of a targeted quantitative approach by which predetermined protein sets are first identified and subsequently quantified at high sensitivity reliably in multiple samples. This approach consists of three steps. First, the proteome is extensively mapped out by multidimensional fractionation and tandem mass spectrometry, and the data generated are assembled in the PeptideAtlas database. Second, based on this proteome map, peptides uniquely identifying the proteins of interest, proteotypic peptides, are selected, and multiple reaction monitoring (MRM) transitions are established and validated by MS2 spectrum acquisition. This process of peptide selection, transition selection, and validation is supported by a suite of software tools, TIQAM (Targeted Identification for Quantitative Analysis by MRM), described in this study. Third, the selected target protein set is quantified in multiple samples by MRM. Applying this approach we were able to reliably quantify low abundance virulence factors from cultures of the human pathogen Streptococcus pyogenes exposed to increasing amounts of plasma. The resulting quantitative protein patterns enabled us to clearly define the subset of virulence proteins that is regulated upon plasma exposure.Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring.Lange Vinzenz V, Malmström Johan A JA, Didion John J, King Nichole L NL, Johansson Björn P BP, Schäfer Juliane J, Rameseder Jonathan J, Wong Chee-Hong CH, Deutsch Eric W EW, Brusniak Mi-Youn MY, Bühlmann Peter P, Björck Lars L, Domon Bruno B, Aebersold Ruedi RMultiple Reaction Monitoring, Pathogenicity Factors, MRM., Virulence Factor, count in organism, Streptococcus scarlatinae, Micrococcus scarlatinae, Flesh-Eating Bacteria, Virulence, Flesh-Eating, Factors, determination, Streptococcus Group A, Streptococcus pyrogenes, chemical analysis, Streptococcus hemolyticus, Pathogenicity Factor, Pathogenicity, number, assay, Factor, Bacteria, Streptococcus erysipelatos, presenceMBNL, EXP42., EXP35, EXP, EXP40Virulence, degree (angle), Tandem, methionine aminopeptidase activity, determination, Streptococcus Group A, selection process, Blood, protein, Mass Spectrometry Mass Spectrometry, infectivity, dmTAF[[II]]230, peptide, Polypeptides, Techniques, peptido, Method, 2, Software Engineering, Analysis, protein aggregate, Computer Program, peptidase M activity, Mass Spectrum Analysis, adenomas, rabGAPLP, Fresh Frozen Plasmas, Fresh Frozen, viral infection, L-methionine aminopeptidase activity, me75, Man (Taxonomy), TFIID TAF250, peptides, Biology, Analyses, cel, Streptococcus pyrogenes, developmental field, Open, E430039A18Rik, Computer Programs and Programming, RabGAP-5, Mass Spectrometry, procedures, D17Mit170, T1, allergic reaction, Pathogenicity Factors, reaction, Methodological Studies, RUSC3, Streptococcus hemolyticus, s, plasma, dTAF[[II]]230, Frozen Plasma, anatomical protrusion, Modern, MYH-associated polyposis, TAF200, autosomal recessive familial adenomatous polyposis, Maps, future organ, TAFII-250, Procedure, TAF250/230, Tl3, Streptococcus erysipelatos, Tl2, Plasmas, Spectrum Analysis, Source Softwares, Software Tools, Multiple Reaction Monitoring, Programs, Spectroscopy, Program, Computer Applications, Virulence Factor, Streptococcus scarlatinae, TAFII250, Computer Applications Software, Computer Applications Softwares, Pathogenicity, Softwares, autosomal recessive, RUTBC3, Software Applications, Factors, Flesh-Eating, HLA-DR-associated protein II, MS/MS, Source Software, Spectrometry, Methodological, exposed, CG17603, TAF[[II]], Methodological Study, human, RABGAP5, Applications, Taf250, Specificity and Sensitivity, spine, SR3-5, multiple colorectal, Polypeptide, Proteomes, TAF230, Computer Software Applications, Fresh, d230, human being, Procedures, Fresh Frozen Plasma, Peptidomics, number, Gene, dTAFII250, Spectrum Analyses, Computer, protein-containing complex, EfW1, presence, protrusion, Human, organ field, Homo sapiens, dmTAF1, Taf230, sensitive, Gene Products, Mass, Studies, Pathogenicity Factor, field, Low, Technique, sensitivity, Man, familial adenomatous polyposis, Mass Spectroscopy, MAP, Application, TAF250, study, Open Source Softwares, Taf200, Micrococcus scarlatinae, Blood Plasma, Flesh-Eating Bacteria, dTAF[[II]]250, MRM, cell, MS2, Software Application, familial adenomatous polyposis 2, Open Source Software, Taf1p, Bacteria, CD156, Computer Software Application, autosomal recessive multiple colorectal adenomas, Study, dTAF250, extruding from, Tools, Blood Plasmas, Sensitivity, peptidos, TAF, Applications Software, Open Source, TAF[[II]]250, MUTYH-Associated Polyposis, Computer Software, cou, protein complex, exits through, Proteins, total expressed protein, l(3)84Ab, BG:DS00004.13, Factor, Cell, Peptide, Tool, dTAF230, polypeptide, Frozen Plasmas, count in organism, Software Tool, MS, Lr, native protein, p230, Systems, Protein, chemical analysis, TAF[[II]]250/230, TFIID, techniques, Software, Mass Spectrum Analyses, tandem MS, Data Base, plasma., Taf[[II]]250, Plasma, Mass Spectrum, TAF[[II]]230, Engineering, Specificity, portion of plasma, TAF[II]250, arc degree, Mass Spectrometry-Mass Spectrometry, MYH-Associated Polyposis, CD156a, Protein Gene Products, Computer Programs, Gene Proteins, DmelCG17603, Applications Softwares, Modern Man, Bra, MAP syndrome, Peptid, virulence, assay, FAP2, methodology, TAF1, colorectal adenomatous polyposisfalseStrepPyogenes_FFE2_LTQStreptococcus pyogenenes FFE LTQ exp2008-12-312016-03-29PAe00028518408245IPI00019359IPI0022032715674254156742551567426115674263156742641567427815674283156742861567428715674289156742921567429315674294156742971567429815674299156743011567430215674303156743041567430615674308156743111567431215674313156743151567431915674321156743221567433515674339156743421567436515674366156743671567436815674369156743781567438915674390156743941567440315674409156744141567442015674424156744301567444015674448156744491567445115674452156744531567446615674475156744761567448115674482156744831567449115674499156745031567450415674518156745271567453515674539156745451567454715674549156745631567456715674570156745731567457615674579156745801567458115674582156745861567460515674611156746151567462115674658156746591567466715674674156746761567467815674679156746821567468815674691156746921567469415674695156746971567470015674715156747501567477115674775156747771567478415674785156747981567480015674804156748081567481415674815156748201567482515674826156748271567482915674843156748451567484615674853156748601567487115674875156748761567487715674885156748871567488815674893156748951567490615674910156749131567491515674917156749181567492315674925156749271567493215674933156749341567494715674953156749541567495515674960156749881567502515675026156750271567502815675029156750301567503515675050156750621567506415675065156750831567510015675102156751051567510815675113156751181567512215675127156751281567513115675133156751451567514815675162156751651567517715675185156751881567519215675196156751991567520015675212156752191567522015675221156752251567523215675235156752361567524715675259156752611567526215675264156752731567527615675290156752921567530315675304156753051567530615675313156753141567531715675334156753351567533715675343156753441567539115675394156753971567540715675411156754141567541515675418156754201567542115675426156754271567542815675438156754441567544715675460156754631567546415675471156754921567549615675501156755021567550615675510156755131567551615675521156755221567552415675527156755291567553915675544156755461567554715675548156755491567555415675555156755571567557015675571156755741567558015675587156755911567559215675596156755971567559815675599156756001567560115675602156756051567560615675607156756141567561515675616156756391567565015675657156756581567566215675669156756721567567915675681156756841567568815675696156756971567569915675700156757021567570515675707156757081567570915675719156757351567573615675739156757561567575815675760156757641567579215675795156757961567579815675799156758071567580815675809156758101567582815675832156758331567583615675837156758381567584915675850156758511567586015675864156758661567587115675893156758981567589915675910156759141567591815675930156759391567594015675942156759451567594615675947