Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses
Open accessAbstract
Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is the main method for high-throughput identification and quantification of peptides and inferred proteins. Within this field, data-independent acquisition (DIA) combined with peptide-centric scoring, as exemplified by the technique SWATH-MS, has emerged as a scalable method to achieve deep and consistent proteome coverage across large-scale data sets. We demonstrate that statistical concepts developed for discovery proteomics based on spectrum-centric scoring can be adapted to large-scale DIA experiments that have been analyzed with peptide-centric scoring strategies, and we provide guidance on their application. We show that optimal tradeoffs between sensitivity and specificity require careful considerations of the relationship between proteins in the samples and proteins represented in the spectral library. We propose the application of a global analyte constraint to prevent the accumulation of false positives across large-scale data sets. Furthermore, to increase the quality and reproducibility of published proteomic results, well-established confidence criteria should be reported for the detected peptide queries, peptides and inferred proteins.
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When FDR was controlled only at peptide query level and not protein level, and only sample-by-sample and not in the global context, the accumulation of new peak groups steadily increased, indicating likely accumulation of false positives.
“The accumulation of new peak groups steadily increased across the data set, indicating a likely accumulation of false positives and, highlighting the importance of appropriate global FDR control55, 56.”
From Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry (2017) · cites this paper as [55]
The result of this study, focused on assessing variation in data acquisition, is paralleled by concurrent improvements in robustness of data analysis tools, methods for error rate control, and sample preparation techniques.
“The result of our study, focused on assessing variation in data acquisition, is paralleled by concurrent improvements in the robustness of data analysis tools39, methods for error rate control55, and sample preparation techniques43.”
From Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry (2017) · cites this paper as [55]
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Self-citation
- Authors
- Rosenberger, G., Bludau, I., Schmitt, U., Heusel, M., Hunter, C. L., Liu, Y., MacCoss, M. J., MacLean, B. X., Nesvizhskii, A. I., Pedrioli, P. G. A., Reiter, L., Röst, H. L., Tate, S., Ting, Y. S., Collins, B. C., & Aebersold, R.
- Affiliations
- University of Zurich (CH)
- ETH Zurich (CH)
- University of Washington (US)
- University of Michigan (US)
- Biognosys (Switzerland) (CH)
- Sciex (Canada) (CA)
- Corresponding author
- Collins, Ben C
- Aebersold, Ruedi
- ORCID
- Venue
- Nature Methods
- Published
- 2017-08-21
- Volume
- 14
- Issue
- 9
- Pages
- 921-927
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC5581544
- OpenAlex
- W2745376284
- Cited by
- 203
- References
- 50
- Citations by year
- 2026: 15 · 2025: 11 · 2024: 19 · 2023: 19 · 2022: 27 · 2021: 27 · 2020: 36 · 2019: 25 · 2018: 20 · 2017: 4
- FWCI
- 11.46
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Research Portal (Queen's University Belfast) (submittedVersion, other-oa)
- Funders
- National Science Foundation
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (P2EZP3, 31003A, 130530, 162268, 161435)
- Eidgenössische Technische Hochschule Zürich
- Institut Mérieux (PZ00P3_161435)
- National Institutes of Health
- National Institute of General Medical Sciences (P41GM103533, R01GM094231)
- FP7 Ideas: European Research Council (233226)
- 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 › Metabolomics and Mass Spectrometry Studies
- Keywords
- data-independent acquisition, false discovery rate, SWATH-MS, spectral library, large-scale proteomics, targeted proteomics
- MeSH terms
- Computer Simulation, Data Interpretation, Statistical, Peptide Mapping, Proteins, Sensitivity and Specificity, Mass Spectrometry, Reproducibility of Results, Models, Statistical, Sequence Analysis, Protein, High-Throughput Screening Assays
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