Ultra-fast proteomics with Scanning SWATH #MMPMID33767396
Messner CB; Demichev V; Bloomfield N; Yu JSL; White M; Kreidl M; Egger AS; Freiwald A; Ivosev G; Wasim F; Zelezniak A; Jurgens L; Suttorp N; Sander LE; Kurth F; Lilley KS; Mulleder M; Tate S; Ralser M
Nat Biotechnol 2021[Jul]; 39 (7): 846-854 PMID33767396show ga
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 microl 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.
free
free
free
Nat+Biotechnol 2021 ; 39 (7): 846-854
