Ultra-fast proteomics with Scanning SWATHMore about Open Access at the Crick
Authors listChristoph Messner Vadim Demichev Nic Bloomfield Jason SL Yu Matthew White Marco Kreidl Anna Sophia Egger Anja Freiwald Gordana Ivosev Fras Wasim Aleksej Zelezniak Linda Jürgens Norbert Suttorp Leif Erik Sander Florian Kurth Kathryn S Lilley Michael Mülleder Stephen Tate Markus Ralser
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.
Journal Nature Biotechnology
Issue number 7