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

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

  • Collins BC Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland.
  • Hunter CL SCIEX, 1201 Radio Road, Redwood City, CA, 94065, USA.
  • Liu Y Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland.
  • Schilling B Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA, 94945, USA.
  • Rosenberger G Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland.
  • Bader SL Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA.
  • Chan DW Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA.
  • Gibson BW Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA, 94945, USA.
  • Gingras AC Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, M5G 1X5, Ontario, Canada.
  • Held JM Departments of Medicine and Anesthesiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO, 63110, USA.
  • Hirayama-Kurogi M Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan.
  • Hou G Proteomics Division, BGI-Shenzhen, Shenzhen, 518083, China.
  • Krisp C Department of Chemistry and Biomolecular Sciences, Australian Proteome Analysis Facility (APAF), Macquarie University, Sydney, 2109, Australia.
  • Larsen B Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, M5G 1X5, Ontario, Canada.
  • Lin L Proteomics Division, BGI-Shenzhen, Shenzhen, 518083, China.
  • Liu S Proteomics Division, BGI-Shenzhen, Shenzhen, 518083, China.
  • Molloy MP Department of Chemistry and Biomolecular Sciences, Australian Proteome Analysis Facility (APAF), Macquarie University, Sydney, 2109, Australia.
  • Moritz RL Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA.
  • Ohtsuki S Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan.
  • Schlapbach R Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland.
  • Selevsek N Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland.
  • Thomas SN Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA.
  • Tzeng SC Departments of Medicine and Anesthesiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO, 63110, USA.
  • Zhang H Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA.
  • Aebersold R Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland. aebersold@imsb.biol.ethz.ch.
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  • 2017-08-23
Published in:
  • Nature communications. - 2017
HEK293 Cells
Humans
Laboratories
Laboratory Proficiency Testing
Mass Spectrometry
Proteome
Proteomics
Reproducibility of Results
English 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.SWATH-mass spectrometry consists of a data-independent acquisition and a targeted data analysis strategy that aims to maintain the favorable quantitative characteristics on the scale of thousands of proteins. Here, using data generated by eleven groups worldwide, the authors show that SWATH-MS is capable of generating highly reproducible data across different laboratories.
Language
  • English
Open access status
gold
Identifiers
Persistent URL
https://folia.unifr.ch/global/documents/220702
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