Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry

Ben C. Collins, Christie L. Hunter, Yansheng Liu, Birgit Schilling, George Rosenberger, Samuel L. Bader, Daniel W. Chan, Bradford W. Gibson, Anne-Claude Gingras, Jason M. Held, Mio Hirayama-Kurogi, Guixue Hou, Christoph Krisp, Brett Larsen, Liang Lin, Siqi Liu, Mark P. Molloy, Robert L. Moritz, Sumio Ohtsuki, Ralph Schlapbach, Nathalie Selevsek, Stefani N. Thomas, Shin-Cheng Tzeng, Hui Zhang and Ruedi Aebersold ()
Additional contact information
Ben C. Collins: Institute of Molecular Systems Biology
Christie L. Hunter: SCIEX
Yansheng Liu: Institute of Molecular Systems Biology
Birgit Schilling: Buck Institute for Research on Aging
George Rosenberger: Institute of Molecular Systems Biology
Samuel L. Bader: Institute for Systems Biology
Daniel W. Chan: Johns Hopkins University School of Medicine
Bradford W. Gibson: Buck Institute for Research on Aging
Anne-Claude Gingras: Lunenfeld-Tanenbaum Research Institute, Sinai Health System
Jason M. Held: Washington University School of Medicine, 660 South Euclid Avenue
Mio Hirayama-Kurogi: Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi
Guixue Hou: Proteomics Division, BGI-Shenzhen
Christoph Krisp: Macquarie University
Brett Larsen: Lunenfeld-Tanenbaum Research Institute, Sinai Health System
Liang Lin: Proteomics Division, BGI-Shenzhen
Siqi Liu: Proteomics Division, BGI-Shenzhen
Mark P. Molloy: Macquarie University
Robert L. Moritz: Institute for Systems Biology
Sumio Ohtsuki: Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi
Ralph Schlapbach: ETH Zurich/University of Zurich
Nathalie Selevsek: ETH Zurich/University of Zurich
Stefani N. Thomas: Johns Hopkins University School of Medicine
Shin-Cheng Tzeng: Washington University School of Medicine, 660 South Euclid Avenue
Hui Zhang: Johns Hopkins University School of Medicine
Ruedi Aebersold: Institute of Molecular Systems Biology

Nature Communications, 2017, vol. 8, issue 1, 1-12

Abstract: Abstract Quantitative proteomics employing mass spectrometry is an indispensable tool in life science research. Targeted proteomics has emerged as a powerful approach for reproducible quantification but is limited in the number of proteins quantified. SWATH-mass spectrometry consists of data-independent acquisition and a targeted data analysis strategy that aims to maintain the favorable quantitative characteristics (accuracy, sensitivity, and selectivity) of targeted proteomics at large scale. While previous SWATH-mass spectrometry studies have shown high intra-lab reproducibility, this has not been evaluated between labs. In this multi-laboratory evaluation study including 11 sites worldwide, we demonstrate that using SWATH-mass spectrometry data acquisition we can consistently detect and reproducibly quantify >4000 proteins from HEK293 cells. Using synthetic peptide dilution series, we show that the sensitivity, dynamic range and reproducibility established with SWATH-mass spectrometry are uniformly achieved. This study demonstrates that the acquisition of reproducible quantitative proteomics data by multiple labs is achievable, and broadly serves to increase confidence in SWATH-mass spectrometry data acquisition as a reproducible method for large-scale protein quantification.

Date: 2017
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DOI: 10.1038/s41467-017-00249-5

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