Journal Article

Ultra-fast proteomics with Scanning SWATH

Sander, Leif Erik, Demichev, Vadim, Ivosev, Gordana, Kreidl, Marco, Suttorp, Norbert, Lilley, Kathryn S., Yu, Jason S. L., Messner, Christoph B., White, Matthew, Zelezniak, Aleksej, Freiwald, Anja, Kurth, Florian, Mülleder, Michael, Bloomfield, Nic, Wasim, Fras, Jürgens, Linda, Egger, Anna-Sophia, Tate, Stephen, Ralser, Markus

2021

Overview

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. Scanning SWATH increases the speed and selectivity of proteomics.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 631/45/475 / 631/61/475 / Acceleration / Agriculture / Algorithms / Analysis / Antifungal agents / Arabidopsis - metabolism / Azoles / Bioinformatics / Biomarkers / Biomarkers - metabolism / Biomedical and Life Sciences / Biomedical Engineering/Biotechnology / Biomedicine / Biotechnology / Cell Line / Chromatography / Comparative analysis / COVID-19 / COVID-19 - blood / COVID-19 - diagnosis / Drug screening / Heterocyclic compounds / Humans / Life Sciences / Mass spectrometry / Mass spectroscopy / Methods / Mode of action / Peptides - analysis / Precursors / Proteome - analysis / Proteomes / Proteomics / Proteomics - methods / Saccharomyces cerevisiae - metabolism / Saccharomyces cerevisiae Proteins - metabolism / Scanning / Selectivity / Severity of Illness Index / Statins / Tandem Mass Spectrometry