Ultra-fast proteomics with Scanning SWATH

10.1038/s41587-021-00860-4

Nature Biotechnology

6th April 2021

Accurate quantification of the proteome remains challenging for large sample series and longitudinal experiments. We report a data-independent acquisition method, Scanning SWATH, that accelerates mass spectrometric (MS) duty cycles, yielding quantitative proteomes in combination with short gradients and high-flow (800 µl min–1) chromatography. Exploiting a continuous movement of the precursor isolation window to assign precursor masses to tandem mass spectrometry (MS/MS) fragment traces, Scanning SWATH increases precursor identifications by ~70% compared to conventional data-independent acquisition (DIA) methods on 0.5–5-min chromatographic gradients. We demonstrate the application of ultra-fast proteomics in drug mode-of-action screening and plasma proteomics. Scanning SWATH proteomes capture the mode of action of fungistatic azoles and statins. Moreover, we confirm 43 and identify 11 new plasma proteome biomarkers of COVID-19 severity, advancing patient classification and biomarker discovery. Thus, our results demonstrate a substantial acceleration and increased depth in fast proteomic experiments that facilitate proteomic drug screens and clinical studies.

Author list:

Attributions

  1. Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
  2. Department of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
  3. Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK.
  4. SCIEX, Concord, Ontario, Canada.
  5. Core Facility – High Throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
  6. Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
  7. Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
  8. Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine & I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg,

Germany.

These authors contributed equally: Christoph B. Messner, Vadim Demichev

 

Authors

Christoph B. Messner1,2,9, Vadim Demichev 1,2,3,9, Nic Bloomfield4, Jason S. L. Yu1, Matthew White1, Marco Kreidl1, Anna-Sophia Egger1, Anja Freiwald2,5, Gordana Ivosev4, Fras Wasim4, Aleksej Zelezniak1,6, Linda Jürgens7, Norbert Suttorp7, Leif Erik Sander 7 , Florian Kurth 7,8, Kathryn S. Lilley 3, Michael Mülleder5, Stephen Tate4 and Markus Ralser * 1,2