A multicenter study benchmarks software tools for label-free proteome quantification
Open accessAbstract
Consistent and accurate quantification of proteins by mass spectrometry (MS)-based proteomics depends on the performance of instruments, acquisition methods and data analysis software. In collaboration with the software developers, we evaluated OpenSWATH, SWATH 2.0, Skyline, Spectronaut and DIA-Umpire, five of the most widely used software methods for processing data from sequential window acquisition of all theoretical fragment-ion spectra (SWATH)-MS, which uses data-independent acquisition (DIA) for label-free protein quantification. We analyzed high-complexity test data sets from hybrid proteome samples of defined quantitative composition acquired on two different MS instruments using different SWATH isolation-window setups. For consistent evaluation, we developed LFQbench, an R package, to calculate metrics of precision and accuracy in label-free quantitative MS and report the identification performance, robustness and specificity of each software tool. Our reference data sets enabled developers to improve their software tools. After optimization, all tools provided highly convergent identification and reliable quantification performance, underscoring their robustness for label-free quantitative proteomics.
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A recent study comparing software tools for DIA data using peptide-centric or spectrum-centric approaches demonstrated very similar qualitative and quantitative results on a benchmarking data set.
“A recent study comparing software tools for the analysis of DIA data using either peptide-centric or spectrum-centric approaches has demonstrated that very similar qualitative and quantitative results can be obtained when analyzing a benchmarking data set39.”
From Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry (2017) · cites this paper as [39]
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 [39]
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References 49 · Cited by 346
- Authors
- Navarro, P., Kuharev, J., Gillet, L. C., Bernhardt, O. M., MacLean, B., Röst, H. L., Tate, S. A., Tsou, C.-C., Reiter, L., Distler, U., Rosenberger, G., Perez-Riverol, Y., Nesvizhskii, A. I., Aebersold, R., & Tenzer, S.
- Affiliations
- University Medical Center of the Johannes Gutenberg University Mainz (DE)
- ETH Zurich (CH)
- Biognosys (Switzerland) (CH)
- University of Washington (US)
- University of Michigan (US)
- University of Zurich (CH)
- Corresponding author
- Navarro, Pedro
- Tenzer, Stefan
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2016-10-03
- Volume
- 34
- Issue
- 11
- Pages
- 1130-1136
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC5120688
- OpenAlex
- W2529750106
- Cited by
- 346
- References
- 49
- Citations by year
- 2026: 22 · 2025: 24 · 2024: 23 · 2023: 43 · 2022: 39 · 2021: 48 · 2020: 48 · 2019: 40 · 2018: 32 · 2017: 24 · 2016: 2 · 2014: 1
- FWCI
- 16.28
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (166435, 162268)
- Biotechnology and Biological Sciences Research Council (BB/K01997X/1)
- National Institute of General Medical Sciences (R01GM094231)
- 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
- label-free quantitative proteomics, SWATH-MS, data-independent acquisition, software benchmarking, skyline, Spectronaut
- MeSH terms
- Algorithms, Sensitivity and Specificity, Software, Mass Spectrometry, Staining and Labeling, Reproducibility of Results, Benchmarking, Proteome, Internationality
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