A HUPO test sample study reveals common problems in mass spectrometry–based proteomics (original) (raw)

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NOTE: In the version of this article initially published, the author name Steven A Carr was spelled incorrectly, and the name of an organization described in the text, the HUPO Proteomics Standards Initiative (PSI), was given incorrectly. These errors have been corrected in the PDF and HTML versions of this article.

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Acknowledgements

Supported in part by Canadian Institutes of Health Research to the HUPO Head Quarters (S. Ouellette) for coordination of this HUPO test sample initiative. A.W.B. and C.E.A. were supported by Genome Quebec and McGill University. We thank D. Juncker, G. Temple, J. van Oostrum, G. Omenn, K. Colwill, J. Langridge and M. Hallett for their comments on the manuscript, and D.M. Desiderio for helpful comments on the manuscript. This test sample effort builds on pioneering efforts from several other groups and especially Association of Biomolecular Resource Facilities. This study is a HUPO test sample initiative and HUPO welcomes collaborative efforts to benefit proteomics. We acknowledge the following sources of grant support: E.W.D. is supported by the National Heart, Lung and Blood Institute, National Institutes of Health (NIH), under contract N01-HV-28179; the University of California, Los Angeles Burnham Institute for Medical Research NIH grant number RR020843; University of California, Los Angeles (National Heart, Lung and Blood Institute P01-008111); University of Michigan, NIH P41RR018627; Beijing Proteome Research Center, affiliated with The Beijing Institute of Radiation Medicine for National Key Programs for Basic Research grant 2006CB910801 and Hi-Tech Research grant 2006AA02A308. We acknowledge access and use of The University College Dublin Conway Mass Spectrometry Resource instrumentation, supported by Science Foundation, Ireland grant 04/RPI/B499. PRIDE, J.A.V. is a postdoctoral fellow of the “Especialización en Organismos Internacionales” program from the Spanish Ministry of Education and Science. L.M. is supported by the “ProDaC” grant LSHG-CT-2006-036814 of the EU. Samuel Lunenfeld Research Institute, Mount Sinai, Toronto is supported by Genome Canada through Ontario Genomics Institute. J.A.V. and L.M. thank H. Hermjakob and R. Apweiler for their support. A.W.B. thanks L. Roy and Z. Bencsath-Makkai for help in data submission and analysis.

Author information

Authors and Affiliations

  1. Department of Anatomy and Cell Biology, McGill University, Montreal, Canada
    Alexander W Bell, Catherine E Au & John J M Bergeron
  2. The Institute for Systems Biology, Seattle, Washington, USA
    Eric W Deutsch
  3. Department of Biomedical Engineering, McGill University, Montreal, Canada
    Robert E Kearney
  4. Biomedical Research Centre, University of British Columbia, Vancouver, Canada
    Ron Beavis
  5. Division Diabetes, Endocrinology and Metabolic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
    Salvatore Sechi
  6. The Research Institute of the McGill University Health Centre and the Department of Medicine, McGill University, Montreal, Canada
    Tommy Nilsson
  7. Verdezyne, Inc., Carlsbad, California, USA
    Thomas A Beardslee
  8. BioGrammatics Incorporated, Carlsbad, California, USA
    Thomas Chappell
  9. Invitrogen Corporation, Carlsbad, California, USA
    Gavin Meredith, Mahbod Hajivandi, Marshall Pope & Paul Predki
  10. Allergan, Irvine, California, USA
    Peter Sheffield
  11. Ambry Genetics, Aliso Viejo, California, USA
    Phillip Gray
  12. Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
    Majlinda Kullolli, Marina Hincapie & William S Hancock
  13. State Key Laboratory of Proteomics, Beijing Proteome Research Center, Changping District, Beijing, China
    Wei Jia, Lina Song, Lei Li, Junying Wei, Bing Yang, Jinglan Wang, Wantao Ying, Yangjun Zhang, Yun Cai, Xiaohong Qian & Fuchu He
  14. Bochum University, Ruhr-Universitaet Bochum, Bochum, Germany
    Helmut E Meyer, Christian Stephan, Martin Eisenacher, Katrin Marcus, Elmar Langenfeld & Caroline May
  15. Proteomics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
    Steven A Carr & Rushdy Ahmad
  16. Burnham Institute for Medical Research, La Jolla, California, USA
    Wenhong Zhu & Jeffrey W Smith
  17. Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
    Samir M Hanash, Jason J Struthers, Hong Wang & Qing Zhang
  18. Department of Oncology, Georgetown University, Washington, DC, USA
    Yanming An & Radoslav Goldman
  19. Göteborg Proteomics Centre: The Proteomics Core Facility, Sahlgrenska Academy, University of Göteborg, Göteborg, Sweden
    Elisabet Carlsohn & Sjoerd van der Post
  20. Harvard Partners Center for Genetics and Genomics, Cambridge, Massachusetts, USA
    Kenneth E Hung, Kenneth Parker & Raju Kucherlapati
  21. Thermo-Fisher BRIMS Center, Cambridge, Massachusetts, USA
    David A Sarracino & Bryan Krastins
  22. Proteomics Platform, Quebec Genomic Center, Laval University Medical Research Center, Quebec, Canada
    Sylvie Bourassa
  23. Health and Environment Unit, Laval University Medical Research Center, Quebec, Canada
    Guy G Poirier
  24. Joint Proteomics Laboratory, Ludwig Institute for Cancer Research and The Walter & Eliza Hall Institute for Medical Research, Parkville, Australia
    Eugene Kapp, Heather Patsiouras, Robert Moritz & Richard Simpson
  25. Genizon BioSciences Incorporated, Saint Laurent, Canada
    Benoit Houle
  26. McGill University and Genome Quebec Innovation Centre, Montréal, Canada
    Sylvie LaBoissiere
  27. Ontario Cancer Biomarker Network, MaRS Centre, Toronto, Canada
    Pavel Metalnikov
  28. Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
    Vivian Nguyen & Tony Pawson
  29. Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA
    Catherine C L Wong, Daniel Cociorva & John R Yates III
  30. Department of Biochemistry, University of Alberta, Edmonton, Canada
    Michael J Ellison, Ana Lopez-Campistrous & Paul Semchuk
  31. Departments of Physiology, Medicine and Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
    Yueju Wang & Peipei Ping
  32. Proteome Research Centre, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
    Giuliano Elia, Michael J Dunn & Kieran Wynne
  33. Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
    Angela K Walker, John R Strahler, Philip C Andrews & Jayson A Falkner
  34. Clinical Proteomics Facility, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
    Brian L Hood, William L Bigbee & Thomas P Conrads
  35. Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
    Brian L Hood & Thomas P Conrads
  36. Department of Pathology, University of Pittsburgh School of Medicine, Magee-Womens Research Institute, Pittsburgh, Pennsylvania, USA
    William L Bigbee
  37. University of Victoria, Victoria, Canada
    Derek Smith & Christoph H Borchers
  38. Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
    Gilles A Lajoie & Sean C Bendall
  39. The Wistar Institute, Philadelphia, Pennsylvania, USA
    Kaye D Speicher & David W Speicher
  40. Department of Biochemistry and Functional Proteomics, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
    Masanori Fujimoto & Kazuyuki Nakamura
  41. Yonsei Proteome Research Center, Yonsei University, Sudaemoon-ku, Seoul, Korea
    Young-Ki Paik, Sang Yun Cho, Min-Seok Kwon, Hyoung-Joo Lee, Seul-Ki Jeong & An Sung Chung
  42. Agilent Technologies Incorporated, Santa Clara, California, USA
    Christine A Miller & Rudolf Grimm
  43. Applied Biosystems, Foster City, California, USA
    Katy Williams
  44. Waters Corporation, Milford, Massachusetts, USA
    Craig Dorschel
  45. EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Lennart Martens & Juan Antonio Vizcaíno

Authors

  1. Alexander W Bell
  2. Eric W Deutsch
  3. Catherine E Au
  4. Robert E Kearney
  5. Ron Beavis
  6. Salvatore Sechi
  7. Tommy Nilsson
  8. John J M Bergeron

Consortia

HUPO Test Sample Working Group

Contributions

A.W.B. coordinated all steps of the study. C.E.A., T.N. and J.J.M.B. coordinated data analysis and the final manuscript. E.W.D., R.B. and R.K. did the centralized analysis of the collective data retrieved from the raw data supplied from each lab to Tranche. S.A.C., P.P., L.M., E.K., C.D., S.S., X.Q., K.W., T.P.C., K.P. and T.A.B. provided comments. Invitrogen prepared, designed and distributed the test sample proteins.

Corresponding author

Correspondence toJohn J M Bergeron.

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Competing interests

There is a potential to market the test samples used in this study.

Additional information

A full list of authors appears at the end of this paper.

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Bell, A., Deutsch, E., Au, C. et al. A HUPO test sample study reveals common problems in mass spectrometry–based proteomics.Nat Methods 6, 423–430 (2009). https://doi.org/10.1038/nmeth.1333

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