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

Alexander W. Bell, Eric W. Deutsch, Catherine E. Au, Robert E. Kearney, Ron Beavis, Salvatore Sechi, Tommy Nilsson, John J.M. Bergeron, Thomas A. Beardslee, Thomas Chappell, Gavin Meredith, Peter Sheffield, Phillip Gray, Mahbod Hajivandi, Marshall Pope, Paul Predki, Majlinda Kullolli, Marina Hincapie, William S. Hancock, Wei Jia & 82 others Lina Song, Lei Li, Junying Wei, Bing Yang, Jinglan Wang, Wantao Ying, Yangjun Zhang, Yun Cai, Xiaohong Qian, Fuchu He, Helmut E. Meyer, Christian Stephan, Martin Eisenacher, Katrin Marcus, Elmar Langenfeld, Caroline May, Steve A. Carr, Rushdy Ahmad, Wenhong Zhu, Jeffrey W. Smith, Samir M. Hanash, Jason J. Struthers, Hong Wang, Qing Zhang, Yanming An, Radoslav Goldman, Elisabet Carlsohn, Sjoerd van der Post, Kenneth E. Hung, David A. Sarracino, Kenneth Parker, Bryan Krastins, Raju Kucherlapati, Sylvie Bourassa, Guy G. Poirier, Eugene Kapp, Heather Patsiouras, Robert Moritz, Richard Simpson, Benoit Houle, Sylvie LaBoissiere, Pavel Metalnikov, Vivian Nguyen, Tony Pawson, Catherine C.L. Wong, Daniel Cociorva, John R. Yates, Michael J. Ellison, Ana Lopez-Campistrous, Paul Semchuk, Yueju Wang, Peipei Ping, Giuliano Elia, Michael J. Dunn, Kieran Wynne, Angela K. Walker, John R. Strahler, Philip C. Andrews, Brian L. Hood, William L. Bigbee, Thomas P. Conrads, Derek Smith, Christoph H. Borchers, Gilles A. Lajoie, Sean C. Bendall, Kaye D. Speicher, David W. Speicher, Masanori Fujimoto, Kazuyuki Nakamura, Young-Ki Paik, Sang Yun Cho, Min Seok Kwon, Hyoung Joo Lee, Seul Ki Jeong, An Sung Chung, Christine A. Miller, Rudolf Grimm, Katy Williams, Craig Dorschel, Jayson A. Falkner, Lennart Martens, Juan Antonio Vizcaíno

Research output: Contribution to journalArticle

234 Citations (Scopus)

Abstract

We 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.

Original languageEnglish
Pages (from-to)423-430
Number of pages8
JournalNature Methods
Volume6
Issue number6
DOIs
Publication statusPublished - 2009 May 18

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Proteomics
Mass spectrometry
Mass Spectrometry
Peptides
Proteins
Databases
Search Engine
Sampling
Recombinant Proteins
Liquid Chromatography
Liquid chromatography
Mass spectrometers
Search engines
Ions
Contamination

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Bell, A. W., Deutsch, E. W., Au, C. E., Kearney, R. E., Beavis, R., Sechi, S., ... Vizcaíno, J. A. (2009). A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nature Methods, 6(6), 423-430. https://doi.org/10.1038/nmeth.1333
Bell, Alexander W. ; Deutsch, Eric W. ; Au, Catherine E. ; Kearney, Robert E. ; Beavis, Ron ; Sechi, Salvatore ; Nilsson, Tommy ; Bergeron, John J.M. ; Beardslee, Thomas A. ; Chappell, Thomas ; Meredith, Gavin ; Sheffield, Peter ; Gray, Phillip ; Hajivandi, Mahbod ; Pope, Marshall ; Predki, Paul ; Kullolli, Majlinda ; Hincapie, Marina ; Hancock, William S. ; Jia, Wei ; Song, Lina ; Li, Lei ; Wei, Junying ; Yang, Bing ; Wang, Jinglan ; Ying, Wantao ; Zhang, Yangjun ; Cai, Yun ; Qian, Xiaohong ; He, Fuchu ; Meyer, Helmut E. ; Stephan, Christian ; Eisenacher, Martin ; Marcus, Katrin ; Langenfeld, Elmar ; May, Caroline ; Carr, Steve A. ; Ahmad, Rushdy ; Zhu, Wenhong ; Smith, Jeffrey W. ; Hanash, Samir M. ; Struthers, Jason J. ; Wang, Hong ; Zhang, Qing ; An, Yanming ; Goldman, Radoslav ; Carlsohn, Elisabet ; van der Post, Sjoerd ; Hung, Kenneth E. ; Sarracino, David A. ; Parker, Kenneth ; Krastins, Bryan ; Kucherlapati, Raju ; Bourassa, Sylvie ; Poirier, Guy G. ; Kapp, Eugene ; Patsiouras, Heather ; Moritz, Robert ; Simpson, Richard ; Houle, Benoit ; LaBoissiere, Sylvie ; Metalnikov, Pavel ; Nguyen, Vivian ; Pawson, Tony ; Wong, Catherine C.L. ; Cociorva, Daniel ; Yates, John R. ; Ellison, Michael J. ; Lopez-Campistrous, Ana ; Semchuk, Paul ; Wang, Yueju ; Ping, Peipei ; Elia, Giuliano ; Dunn, Michael J. ; Wynne, Kieran ; Walker, Angela K. ; Strahler, John R. ; Andrews, Philip C. ; Hood, Brian L. ; Bigbee, William L. ; Conrads, Thomas P. ; Smith, Derek ; Borchers, Christoph H. ; Lajoie, Gilles A. ; Bendall, Sean C. ; Speicher, Kaye D. ; Speicher, David W. ; Fujimoto, Masanori ; Nakamura, Kazuyuki ; Paik, Young-Ki ; Cho, Sang Yun ; Kwon, Min Seok ; Lee, Hyoung Joo ; Jeong, Seul Ki ; Chung, An Sung ; Miller, Christine A. ; Grimm, Rudolf ; Williams, Katy ; Dorschel, Craig ; Falkner, Jayson A. ; Martens, Lennart ; Vizcaíno, Juan Antonio. / A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. In: Nature Methods. 2009 ; Vol. 6, No. 6. pp. 423-430.
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abstract = "We 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.",
author = "Bell, {Alexander W.} and Deutsch, {Eric W.} and Au, {Catherine E.} and Kearney, {Robert E.} and Ron Beavis and Salvatore Sechi and Tommy Nilsson and Bergeron, {John J.M.} and Beardslee, {Thomas A.} and Thomas Chappell and Gavin Meredith and Peter Sheffield and Phillip Gray and Mahbod Hajivandi and Marshall Pope and Paul Predki and Majlinda Kullolli and Marina Hincapie and Hancock, {William S.} and Wei Jia and Lina Song and Lei Li and Junying Wei and Bing Yang and Jinglan Wang and Wantao Ying and Yangjun Zhang and Yun Cai and Xiaohong Qian and Fuchu He and Meyer, {Helmut E.} and Christian Stephan and Martin Eisenacher and Katrin Marcus and Elmar Langenfeld and Caroline May and Carr, {Steve A.} and Rushdy Ahmad and Wenhong Zhu and Smith, {Jeffrey W.} and Hanash, {Samir M.} and Struthers, {Jason J.} and Hong Wang and Qing Zhang and Yanming An and Radoslav Goldman and Elisabet Carlsohn and {van der Post}, Sjoerd and Hung, {Kenneth E.} and Sarracino, {David A.} and Kenneth Parker and Bryan Krastins and Raju Kucherlapati and Sylvie Bourassa and Poirier, {Guy G.} and Eugene Kapp and Heather Patsiouras and Robert Moritz and Richard Simpson and Benoit Houle and Sylvie LaBoissiere and Pavel Metalnikov and Vivian Nguyen and Tony Pawson and Wong, {Catherine C.L.} and Daniel Cociorva and Yates, {John R.} and Ellison, {Michael J.} and Ana Lopez-Campistrous and Paul Semchuk and Yueju Wang and Peipei Ping and Giuliano Elia and Dunn, {Michael J.} and Kieran Wynne and Walker, {Angela K.} and Strahler, {John R.} and Andrews, {Philip C.} and Hood, {Brian L.} and Bigbee, {William L.} and Conrads, {Thomas P.} and Derek Smith and Borchers, {Christoph H.} and Lajoie, {Gilles A.} and Bendall, {Sean C.} and Speicher, {Kaye D.} and Speicher, {David W.} and Masanori Fujimoto and Kazuyuki Nakamura and Young-Ki Paik and Cho, {Sang Yun} and Kwon, {Min Seok} and Lee, {Hyoung Joo} and Jeong, {Seul Ki} and Chung, {An Sung} and Miller, {Christine A.} and Rudolf Grimm and Katy Williams and Craig Dorschel and Falkner, {Jayson A.} and Lennart Martens and Vizca{\'i}no, {Juan Antonio}",
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Bell, AW, Deutsch, EW, Au, CE, Kearney, RE, Beavis, R, Sechi, S, Nilsson, T, Bergeron, JJM, Beardslee, TA, Chappell, T, Meredith, G, Sheffield, P, Gray, P, Hajivandi, M, Pope, M, Predki, P, Kullolli, M, Hincapie, M, Hancock, WS, Jia, W, Song, L, Li, L, Wei, J, Yang, B, Wang, J, Ying, W, Zhang, Y, Cai, Y, Qian, X, He, F, Meyer, HE, Stephan, C, Eisenacher, M, Marcus, K, Langenfeld, E, May, C, Carr, SA, Ahmad, R, Zhu, W, Smith, JW, Hanash, SM, Struthers, JJ, Wang, H, Zhang, Q, An, Y, Goldman, R, Carlsohn, E, van der Post, S, Hung, KE, Sarracino, DA, Parker, K, Krastins, B, Kucherlapati, R, Bourassa, S, Poirier, GG, Kapp, E, Patsiouras, H, Moritz, R, Simpson, R, Houle, B, LaBoissiere, S, Metalnikov, P, Nguyen, V, Pawson, T, Wong, CCL, Cociorva, D, Yates, JR, Ellison, MJ, Lopez-Campistrous, A, Semchuk, P, Wang, Y, Ping, P, Elia, G, Dunn, MJ, Wynne, K, Walker, AK, Strahler, JR, Andrews, PC, Hood, BL, Bigbee, WL, Conrads, TP, Smith, D, Borchers, CH, Lajoie, GA, Bendall, SC, Speicher, KD, Speicher, DW, Fujimoto, M, Nakamura, K, Paik, Y-K, Cho, SY, Kwon, MS, Lee, HJ, Jeong, SK, Chung, AS, Miller, CA, Grimm, R, Williams, K, Dorschel, C, Falkner, JA, Martens, L & Vizcaíno, JA 2009, 'A HUPO test sample study reveals common problems in mass spectrometry-based proteomics', Nature Methods, vol. 6, no. 6, pp. 423-430. https://doi.org/10.1038/nmeth.1333

A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. / Bell, Alexander W.; Deutsch, Eric W.; Au, Catherine E.; Kearney, Robert E.; Beavis, Ron; Sechi, Salvatore; Nilsson, Tommy; Bergeron, John J.M.; Beardslee, Thomas A.; Chappell, Thomas; Meredith, Gavin; Sheffield, Peter; Gray, Phillip; Hajivandi, Mahbod; Pope, Marshall; Predki, Paul; Kullolli, Majlinda; Hincapie, Marina; Hancock, William S.; Jia, Wei; Song, Lina; Li, Lei; Wei, Junying; Yang, Bing; Wang, Jinglan; Ying, Wantao; Zhang, Yangjun; Cai, Yun; Qian, Xiaohong; He, Fuchu; Meyer, Helmut E.; Stephan, Christian; Eisenacher, Martin; Marcus, Katrin; Langenfeld, Elmar; May, Caroline; Carr, Steve A.; Ahmad, Rushdy; Zhu, Wenhong; Smith, Jeffrey W.; Hanash, Samir M.; Struthers, Jason J.; Wang, Hong; Zhang, Qing; An, Yanming; Goldman, Radoslav; Carlsohn, Elisabet; van der Post, Sjoerd; Hung, Kenneth E.; Sarracino, David A.; Parker, Kenneth; Krastins, Bryan; Kucherlapati, Raju; Bourassa, Sylvie; Poirier, Guy G.; Kapp, Eugene; Patsiouras, Heather; Moritz, Robert; Simpson, Richard; Houle, Benoit; LaBoissiere, Sylvie; Metalnikov, Pavel; Nguyen, Vivian; Pawson, Tony; Wong, Catherine C.L.; Cociorva, Daniel; Yates, John R.; Ellison, Michael J.; Lopez-Campistrous, Ana; Semchuk, Paul; Wang, Yueju; Ping, Peipei; Elia, Giuliano; Dunn, Michael J.; Wynne, Kieran; Walker, Angela K.; Strahler, John R.; Andrews, Philip C.; Hood, Brian L.; Bigbee, William L.; Conrads, Thomas P.; Smith, Derek; Borchers, Christoph H.; Lajoie, Gilles A.; Bendall, Sean C.; Speicher, Kaye D.; Speicher, David W.; Fujimoto, Masanori; Nakamura, Kazuyuki; Paik, Young-Ki; Cho, Sang Yun; Kwon, Min Seok; Lee, Hyoung Joo; Jeong, Seul Ki; Chung, An Sung; Miller, Christine A.; Grimm, Rudolf; Williams, Katy; Dorschel, Craig; Falkner, Jayson A.; Martens, Lennart; Vizcaíno, Juan Antonio.

In: Nature Methods, Vol. 6, No. 6, 18.05.2009, p. 423-430.

Research output: Contribution to journalArticle

TY - JOUR

T1 - A HUPO test sample study reveals common problems in mass spectrometry-based proteomics

AU - Bell, Alexander W.

AU - Deutsch, Eric W.

AU - Au, Catherine E.

AU - Kearney, Robert E.

AU - Beavis, Ron

AU - Sechi, Salvatore

AU - Nilsson, Tommy

AU - Bergeron, John J.M.

AU - Beardslee, Thomas A.

AU - Chappell, Thomas

AU - Meredith, Gavin

AU - Sheffield, Peter

AU - Gray, Phillip

AU - Hajivandi, Mahbod

AU - Pope, Marshall

AU - Predki, Paul

AU - Kullolli, Majlinda

AU - Hincapie, Marina

AU - Hancock, William S.

AU - Jia, Wei

AU - Song, Lina

AU - Li, Lei

AU - Wei, Junying

AU - Yang, Bing

AU - Wang, Jinglan

AU - Ying, Wantao

AU - Zhang, Yangjun

AU - Cai, Yun

AU - Qian, Xiaohong

AU - He, Fuchu

AU - Meyer, Helmut E.

AU - Stephan, Christian

AU - Eisenacher, Martin

AU - Marcus, Katrin

AU - Langenfeld, Elmar

AU - May, Caroline

AU - Carr, Steve A.

AU - Ahmad, Rushdy

AU - Zhu, Wenhong

AU - Smith, Jeffrey W.

AU - Hanash, Samir M.

AU - Struthers, Jason J.

AU - Wang, Hong

AU - Zhang, Qing

AU - An, Yanming

AU - Goldman, Radoslav

AU - Carlsohn, Elisabet

AU - van der Post, Sjoerd

AU - Hung, Kenneth E.

AU - Sarracino, David A.

AU - Parker, Kenneth

AU - Krastins, Bryan

AU - Kucherlapati, Raju

AU - Bourassa, Sylvie

AU - Poirier, Guy G.

AU - Kapp, Eugene

AU - Patsiouras, Heather

AU - Moritz, Robert

AU - Simpson, Richard

AU - Houle, Benoit

AU - LaBoissiere, Sylvie

AU - Metalnikov, Pavel

AU - Nguyen, Vivian

AU - Pawson, Tony

AU - Wong, Catherine C.L.

AU - Cociorva, Daniel

AU - Yates, John R.

AU - Ellison, Michael J.

AU - Lopez-Campistrous, Ana

AU - Semchuk, Paul

AU - Wang, Yueju

AU - Ping, Peipei

AU - Elia, Giuliano

AU - Dunn, Michael J.

AU - Wynne, Kieran

AU - Walker, Angela K.

AU - Strahler, John R.

AU - Andrews, Philip C.

AU - Hood, Brian L.

AU - Bigbee, William L.

AU - Conrads, Thomas P.

AU - Smith, Derek

AU - Borchers, Christoph H.

AU - Lajoie, Gilles A.

AU - Bendall, Sean C.

AU - Speicher, Kaye D.

AU - Speicher, David W.

AU - Fujimoto, Masanori

AU - Nakamura, Kazuyuki

AU - Paik, Young-Ki

AU - Cho, Sang Yun

AU - Kwon, Min Seok

AU - Lee, Hyoung Joo

AU - Jeong, Seul Ki

AU - Chung, An Sung

AU - Miller, Christine A.

AU - Grimm, Rudolf

AU - Williams, Katy

AU - Dorschel, Craig

AU - Falkner, Jayson A.

AU - Martens, Lennart

AU - Vizcaíno, Juan Antonio

PY - 2009/5/18

Y1 - 2009/5/18

N2 - We 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.

AB - We 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.

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Bell AW, Deutsch EW, Au CE, Kearney RE, Beavis R, Sechi S et al. A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nature Methods. 2009 May 18;6(6):423-430. https://doi.org/10.1038/nmeth.1333