title: A multicenter study benchmarks software tools for label-free proteome quantification.
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.
authors.affiliation: Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany.
authors.forename: Pedro
authors.initials: P
authors.lastname: Navarro
authors.affiliation: Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany.
authors.forename: Jörg
authors.initials: J
authors.lastname: Kuharev
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, Eidgenoessische Technische Hochschule (IMSB-ETH) Zurich, Zurich, Switzerland.
authors.forename: Ludovic C
authors.initials: LC
authors.lastname: Gillet
authors.affiliation: Biognosys AG, Schlieren, Switzerland.
authors.forename: Oliver M
authors.initials: OM
authors.lastname: Bernhardt
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: Brendan
authors.initials: B
authors.lastname: MacLean
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, Eidgenoessische Technische Hochschule (IMSB-ETH) Zurich, Zurich, Switzerland.
authors.forename: Hannes L
authors.initials: HL
authors.lastname: Röst
authors.affiliation: AB Sciex, Concord, Ontario, Canada.
authors.forename: Stephen A
authors.initials: SA
authors.lastname: Tate
authors.affiliation: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
authors.forename: Chih-Chiang
authors.initials: CC
authors.lastname: Tsou
authors.affiliation: Biognosys AG, Schlieren, Switzerland.
authors.forename: Lukas
authors.initials: L
authors.lastname: Reiter
authors.affiliation: Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany.
authors.forename: Ute
authors.initials: U
authors.lastname: Distler
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, Eidgenoessische Technische Hochschule (IMSB-ETH) Zurich, Zurich, Switzerland.|PhD Program in Systems Biology, University of Zurich and Eidgenoessische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.
authors.forename: George
authors.initials: G
authors.lastname: Rosenberger
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK.
authors.forename: Yasset
authors.initials: Y
authors.lastname: Perez-Riverol
authors.affiliation: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.|Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA.
authors.forename: Alexey I
authors.initials: AI
authors.lastname: Nesvizhskii
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, Eidgenoessische Technische Hochschule (IMSB-ETH) Zurich, Zurich, Switzerland.|Faculty of Science, University of Zurich, Zurich, Switzerland.
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.affiliation: Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Tenzer
mesh_terms: D000465:Algorithms; D019985:Benchmarking / Q000379:methods* / Q000592:standards*; D038622:Internationality; D013058:Mass Spectrometry / Q000592:standards*; D020543:Proteome / Q000032:analysis / Q000737:chemistry*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D012984:Software / Q000145:classification* / Q000592:standards*; D013194:Staining and Labeling
chemical_list: D020543:Proteome