A HUPO test sample study reveals common problems in mass spectrometry–based proteomics
Open accessAbstract
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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In DDA MS, if the number of precursor ions exceeds the number of precursor selection cycles, precursor selection becomes stochastic and the peptides detected in repeat analyses become irreproducible.
“If the number of precursor ions exceeds the number of precursor selection cycles6, precursor selection becomes stochastic and the peptides detected in repeat analyses become irreproducible.”
From Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry (2017) · cites this paper as [8]
Software and choice of parameters for peak-picking, peptide identification, PTM identification, and quantification remain a significant source of information loss and variability, and software use is often vendor-dependent.
“However the software and choice of parameters for peak-picking, peptide identification, PTM identification, and quantification remains a significant source of information-loss and variability97 and the use of software is often dependent on vendor.”
From Decoding neuroproteomics: integrating the genome, translatome and functional anatomy (2014) · cites this paper as [97]
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- Authors
- HUPO Test Sample Working Group, Bell, A. W., Deutsch, E. W., Au, C. E., Kearney, R. E., Beavis, R., Sechi, S., Nilsson, T., & Bergeron, J. J. M.
- Affiliations
- McGill University (CA)
- Institute for Systems Biology (US)
- University of British Columbia (CA)
- National Institutes of Health (US)
- Research Institute of the McGill University Health Centre (CA)
- Corresponding author
- Bergeron, John J M
- Venue
- Nature Methods
- Published
- 2009-05-17
- Volume
- 6
- Issue
- 6
- Pages
- 423-430
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC2785450
- OpenAlex
- W2088363255
- Cited by
- 351
- References
- 36
- Citations by year
- 2026: 3 · 2025: 6 · 2024: 10 · 2023: 19 · 2022: 10 · 2021: 12 · 2020: 15 · 2019: 16 · 2018: 9 · 2017: 17 · 2016: 18 · 2015: 19 · 2014: 27 · 2013: 28 · 2012: 32
- FWCI
- 20.06
- Type
- journal article
- Language
- en
- Update notices
- erratum (2009-07-01)
- Open access
- bronze
- doi.org
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Ghent University Academic Bibliography (Ghent University) (submittedVersion)
- Scholarship@Western (Western University) (submittedVersion)
- Funders
- McGill University
- Genome Canada
- Ontario Genomics
- Ontario Genomics Institute
- University College Dublin
- National Institutes of Health (n01hv028179-000, RR020843)
- University of California, Los Angeles
- U.S. Public Health Service (P01-008111)
- Canadian Institutes of Health Research
- National Heart, Lung, and Blood Institute (N01 HV028179, N01-HV-28179)
- National Cancer Institute (R01CA120393)
- National Center for Research Resources (RR 020843, U54RR020843, P41RR018627)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced Biosensing Techniques and Applications
- Keywords
- reproducibility, mass spectrometry-based proteomics, interlaboratory comparison, peptide identification, false-negative results, environmental contamination, search engines, recombinant human proteins, tryptic peptides
- MeSH terms
- Chromatography, Liquid, Humans, Peptide Mapping, Sensitivity and Specificity, Mass Spectrometry, Reproducibility of Results, Proteome, Proteomics
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