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Article: A HUPO test sample study reveals common problems in mass spectrometry-based proteomics

TitleA HUPO test sample study reveals common problems in mass spectrometry-based proteomics
Authors
Bell, Alexander W.Deutsch, Eric W.Au, Catherine E.Kearney, Robert E.Beavis, RonSechi, SalvatoreNilsson, TommyBergeron, John J.M.Beardslee, Thomas A.Chappell, ThomasMeredith, GavinSheffield, PeterGray, PhillipHajivandi, MahbodPope, MarshallPredki, PaulKullolli, MajlindaHincapie, MarinaHancock, William S.Jia, WeiSong, LinaLi, LeiWei, JunyingYang, BingWang, JinglanYing, WantaoZhang, YangjunCai, YunQian, XiaohongHe, FuchuMeyer, Helmut E.Stephan, ChristianEisenacher, MartinMarcus, KatrinLangenfeld, ElmarMay, CarolineCarr, Steve A.Ahmad, RushdyZhu, WenhongSmith, Jeffrey W.Hanash, Samir M.Struthers, Jason J.Wang, HongZhang, QingAn, YanmingGoldman, RadoslavCarlsohn, Elisabetvan der Post, SjoerdHung, Kenneth E.Sarracino, David A.Parker, KennethKrastins, BryanKucherlapati, RajuBourassa, SylviePoirier, Guy G.Kapp, EugenePatsiouras, HeatherMoritz, RobertSimpson, RichardHoule, BenoitLaBoissiere, SylvieMetalnikov, PavelNguyen, VivianPawson, TonyWong, Catherine C.L.Cociorva, DanielYates, John R.Ellison, Michael J.Lopez-Campistrous, AnaSemchuk, PaulWang, YuejuPing, PeipeiElia, GiulianoDunn, Michael J.Wynne, KieranWalker, Angela K.Strahler, John R.Andrews, Philip C.Hood, Brian L.Bigbee, William L.Conrads, Thomas P.Smith, DerekBorchers, Christoph H.Lajoie, Gilles A.Bendall, Sean C.Speicher, Kaye D.Speicher, David W.Fujimoto, MasanoriNakamura, KazuyukiPaik, Young KiCho, Sang YunKwon, Min SeokLee, Hyoung JooJeong, Seul KiChung, An SungMiller, Christine A.Grimm, RudolfWilliams, KatyDorschel, CraigFalkner, Jayson A.Martens, LennartVizcaíno, Juan Antonio
Issue Date2009
Citation
Nature Methods, 2009, v. 6, n. 6, p. 423-430 How to Cite?
AbstractWe performed a test sample study to try to identify errors leading to irreproducibility, including incompleteness of peptide sampling, in liquid chromatography-mass spectrometry-based proteomics. We distributed an equimolar test sample, comprising 20 highly purified recombinant human proteins, to 27 laboratories. Each protein contained one or more unique tryptic peptides of 1,250 Da to test for ion selection and sampling in the mass spectrometer. Of the 27 labs, members of only 7 labs initially reported all 20 proteins correctly, and members of only 1 lab reported all tryptic peptides of 1,250 Da. Centralized analysis of the raw data, however, revealed that all 20 proteins and most of the 1,250 Da peptides had been detected in all 27 labs. Our centralized analysis determined missed identifications (false negatives), environmental contamination, database matching and curation of protein identifications as sources of problems. Improved search engines and databases are needed for mass spectrometry-based proteomics.
Persistent Identifierhttp://hdl.handle.net/10722/342356
ISSN
2023 Impact Factor: 36.1
2023 SCImago Journal Rankings: 14.796
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorBell, Alexander W.-
dc.contributor.authorDeutsch, Eric W.-
dc.contributor.authorAu, Catherine E.-
dc.contributor.authorKearney, Robert E.-
dc.contributor.authorBeavis, Ron-
dc.contributor.authorSechi, Salvatore-
dc.contributor.authorNilsson, Tommy-
dc.contributor.authorBergeron, John J.M.-
dc.contributor.authorBeardslee, Thomas A.-
dc.contributor.authorChappell, Thomas-
dc.contributor.authorMeredith, Gavin-
dc.contributor.authorSheffield, Peter-
dc.contributor.authorGray, Phillip-
dc.contributor.authorHajivandi, Mahbod-
dc.contributor.authorPope, Marshall-
dc.contributor.authorPredki, Paul-
dc.contributor.authorKullolli, Majlinda-
dc.contributor.authorHincapie, Marina-
dc.contributor.authorHancock, William S.-
dc.contributor.authorJia, Wei-
dc.contributor.authorSong, Lina-
dc.contributor.authorLi, Lei-
dc.contributor.authorWei, Junying-
dc.contributor.authorYang, Bing-
dc.contributor.authorWang, Jinglan-
dc.contributor.authorYing, Wantao-
dc.contributor.authorZhang, Yangjun-
dc.contributor.authorCai, Yun-
dc.contributor.authorQian, Xiaohong-
dc.contributor.authorHe, Fuchu-
dc.contributor.authorMeyer, Helmut E.-
dc.contributor.authorStephan, Christian-
dc.contributor.authorEisenacher, Martin-
dc.contributor.authorMarcus, Katrin-
dc.contributor.authorLangenfeld, Elmar-
dc.contributor.authorMay, Caroline-
dc.contributor.authorCarr, Steve A.-
dc.contributor.authorAhmad, Rushdy-
dc.contributor.authorZhu, Wenhong-
dc.contributor.authorSmith, Jeffrey W.-
dc.contributor.authorHanash, Samir M.-
dc.contributor.authorStruthers, Jason J.-
dc.contributor.authorWang, Hong-
dc.contributor.authorZhang, Qing-
dc.contributor.authorAn, Yanming-
dc.contributor.authorGoldman, Radoslav-
dc.contributor.authorCarlsohn, Elisabet-
dc.contributor.authorvan der Post, Sjoerd-
dc.contributor.authorHung, Kenneth E.-
dc.contributor.authorSarracino, David A.-
dc.contributor.authorParker, Kenneth-
dc.contributor.authorKrastins, Bryan-
dc.contributor.authorKucherlapati, Raju-
dc.contributor.authorBourassa, Sylvie-
dc.contributor.authorPoirier, Guy G.-
dc.contributor.authorKapp, Eugene-
dc.contributor.authorPatsiouras, Heather-
dc.contributor.authorMoritz, Robert-
dc.contributor.authorSimpson, Richard-
dc.contributor.authorHoule, Benoit-
dc.contributor.authorLaBoissiere, Sylvie-
dc.contributor.authorMetalnikov, Pavel-
dc.contributor.authorNguyen, Vivian-
dc.contributor.authorPawson, Tony-
dc.contributor.authorWong, Catherine C.L.-
dc.contributor.authorCociorva, Daniel-
dc.contributor.authorYates, John R.-
dc.contributor.authorEllison, Michael J.-
dc.contributor.authorLopez-Campistrous, Ana-
dc.contributor.authorSemchuk, Paul-
dc.contributor.authorWang, Yueju-
dc.contributor.authorPing, Peipei-
dc.contributor.authorElia, Giuliano-
dc.contributor.authorDunn, Michael J.-
dc.contributor.authorWynne, Kieran-
dc.contributor.authorWalker, Angela K.-
dc.contributor.authorStrahler, John R.-
dc.contributor.authorAndrews, Philip C.-
dc.contributor.authorHood, Brian L.-
dc.contributor.authorBigbee, William L.-
dc.contributor.authorConrads, Thomas P.-
dc.contributor.authorSmith, Derek-
dc.contributor.authorBorchers, Christoph H.-
dc.contributor.authorLajoie, Gilles A.-
dc.contributor.authorBendall, Sean C.-
dc.contributor.authorSpeicher, Kaye D.-
dc.contributor.authorSpeicher, David W.-
dc.contributor.authorFujimoto, Masanori-
dc.contributor.authorNakamura, Kazuyuki-
dc.contributor.authorPaik, Young Ki-
dc.contributor.authorCho, Sang Yun-
dc.contributor.authorKwon, Min Seok-
dc.contributor.authorLee, Hyoung Joo-
dc.contributor.authorJeong, Seul Ki-
dc.contributor.authorChung, An Sung-
dc.contributor.authorMiller, Christine A.-
dc.contributor.authorGrimm, Rudolf-
dc.contributor.authorWilliams, Katy-
dc.contributor.authorDorschel, Craig-
dc.contributor.authorFalkner, Jayson A.-
dc.contributor.authorMartens, Lennart-
dc.contributor.authorVizcaíno, Juan Antonio-
dc.date.accessioned2024-04-17T07:03:13Z-
dc.date.available2024-04-17T07:03:13Z-
dc.date.issued2009-
dc.identifier.citationNature Methods, 2009, v. 6, n. 6, p. 423-430-
dc.identifier.issn1548-7091-
dc.identifier.urihttp://hdl.handle.net/10722/342356-
dc.description.abstractWe performed a test sample study to try to identify errors leading to irreproducibility, including incompleteness of peptide sampling, in liquid chromatography-mass spectrometry-based proteomics. We distributed an equimolar test sample, comprising 20 highly purified recombinant human proteins, to 27 laboratories. Each protein contained one or more unique tryptic peptides of 1,250 Da to test for ion selection and sampling in the mass spectrometer. Of the 27 labs, members of only 7 labs initially reported all 20 proteins correctly, and members of only 1 lab reported all tryptic peptides of 1,250 Da. Centralized analysis of the raw data, however, revealed that all 20 proteins and most of the 1,250 Da peptides had been detected in all 27 labs. Our centralized analysis determined missed identifications (false negatives), environmental contamination, database matching and curation of protein identifications as sources of problems. Improved search engines and databases are needed for mass spectrometry-based proteomics.-
dc.languageeng-
dc.relation.ispartofNature Methods-
dc.titleA HUPO test sample study reveals common problems in mass spectrometry-based proteomics-
dc.typeArticle-
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1038/nmeth.1333-
dc.identifier.pmid19448641-
dc.identifier.scopuseid_2-s2.0-67349196123-
dc.identifier.volume6-
dc.identifier.issue6-
dc.identifier.spage423-
dc.identifier.epage430-
dc.identifier.eissn1549-1676-
dc.identifier.isiWOS:000266493300012-

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