1. A multicenter study benchmarks software tools for label-free proteome quantification.
- Author
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Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, Röst HL, Tate SA, Tsou CC, Reiter L, Distler U, Rosenberger G, Perez-Riverol Y, Nesvizhskii AI, Aebersold R, and Tenzer S
- Subjects
- Algorithms, Internationality, Proteome analysis, Reproducibility of Results, Sensitivity and Specificity, Staining and Labeling, Benchmarking methods, Benchmarking standards, Mass Spectrometry standards, Proteome chemistry, Software classification, Software standards
- Abstract
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., Competing Interests: The authors declare the following competing financial interests: S.A.T. is employed by SCIEX, O.M.B. and L.R. are employed by Biognosys AG.
- Published
- 2016
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