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

View ORCID ProfileBen 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, Ruedi Aebersold
doi: https://doi.org/10.1101/074567
Ben C. Collins
1 Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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  • ORCID record for Ben C. Collins
Christie L. Hunter
2 SCIEX, 1201 Radio Road, Redwood City, California 94065, USA.
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Yansheng Liu
1 Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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Birgit Schilling
3 Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, California 94945, USA.
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George Rosenberger
1 Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
4 PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland.
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Samuel L. Bader
5 Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA.
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Daniel W. Chan
6 Clinical Chemistry Division, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21231 USA.
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Bradford W. Gibson
3 Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, California 94945, USA.
7 Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA.
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Anne-Claude Gingras
8 Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.
9 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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Jason M. Held
10 Departments of Medicine and Anesthesiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, Missouri 63110, USA.
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Mio Hirayama-Kurogi
11 Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.
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Guixue Hou
12 Proteomics Division, BGI-Shenzhen, Shenzhen, China.
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Christoph Krisp
13 Australian Proteome Analysis Facility (APAF), Department of Chemistry and Biomolecular Sciences, Macquarie University, 2109, Sydney, Australia.
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Brett Larsen
8 Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.
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Liang Lin
12 Proteomics Division, BGI-Shenzhen, Shenzhen, China.
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Siqi Liu
12 Proteomics Division, BGI-Shenzhen, Shenzhen, China.
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Mark P. Molloy
13 Australian Proteome Analysis Facility (APAF), Department of Chemistry and Biomolecular Sciences, Macquarie University, 2109, Sydney, Australia.
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Robert L. Moritz
5 Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA.
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Sumio Ohtsuki
11 Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.
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Ralph Schlapbach
14 Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland.
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Nathalie Selevsek
14 Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland.
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Stefani N. Thomas
6 Clinical Chemistry Division, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21231 USA.
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Shin-Cheng Tzeng
10 Departments of Medicine and Anesthesiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, Missouri 63110, USA.
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Hui Zhang
6 Clinical Chemistry Division, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21231 USA.
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Ruedi Aebersold
1 Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
15 Faculty of Science, University of Zurich, Zurich, Switzerland.
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  • For correspondence: aebersold@imsb.biol.ethz.ch
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Abstract

Quantitative proteomics employing mass spectrometry has become an indispensable tool in basic and applied life science research. Methods based on data-dependent acquisition have proved extremely valuable for qualitative proteome analysis but historically have struggled to achieve reproducible quantitative data if large sample cohorts are comparatively analyzed. Targeted proteomics, most commonly implemented as selected reaction monitoring, has emerged as a powerful alternative and succeeded in providing a data independent approach for reproducible quantitative proteomics data but is limited in the number of proteins quantified. SWATH-MS is a recently introduced technique consisting of a data-independent acquisition and a targeted data analysis strategy that aims to maintain the favorable quantitative characteristics (accuracy, sensitivity, specificity) achieved in targeted proteomics but on the scale of thousands of proteins. While previous SWATH-MS studies have shown high intra-lab reproducibility, this has not been evaluated on an inter-lab basis. In this multi-laboratory evaluation study using data from 11 sites worldwide, we have demonstrated that using SWATH-MS we can consistently detect and quantify more than 4,000 proteins from HEK293 cells and that the quantitative protein data generated across laboratories is reproducible. Using synthetic peptide dilution series, we have shown that the sensitivity, dynamic range and reproducibility established with SWATH-MS methods are also uniformly achieved across labs. This study demonstrates that SWATH-MS is a reproducible and accurate technique that can be confidently deployed for large-scale protein quantification in life science research.

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  • Note: authors from SLB to HZ are listed alphabetically

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Posted September 14, 2016.
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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, Ruedi Aebersold
bioRxiv 074567; doi: https://doi.org/10.1101/074567
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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, Ruedi Aebersold
bioRxiv 074567; doi: https://doi.org/10.1101/074567

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