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

A Corrigendum to this article was published on 01 July 2009

This article has been updated

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.

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Figure 1: Number of tandem mass spectra assigned to tryptic peptides.
Figure 2: Discrepancies between reported data and centralized analysis identify erroneous reporting.

Change history

  • 29 June 2009

    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.

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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 to John J M Bergeron.

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Competing interests

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

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

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–11 , Supplementary Tables 1–5 and 7–11, Supplementary Note, Supplementary Methods (PDF 2922 kb)

Supplementary Table 6

Initial results as submitted by 24 academic laboratories and 3 vendors. (XLS 110 kb)

Supplementary Table 12

Final results and repeat analyses as submitted by 24 academic laboratories and 3 vendors. (PDF 136 kb)

Supplementary Table 13

Peptides identified by centralized analysis of the data. (XLS 607 kb)

Supplementary Table 14

Tranche hash and passphrase codes. (XLS 25 kb)

Supplementary Table 15

Proteins identified by centralized analysis of the data. (XLS 177 kb)

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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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