Minute-scale proteomics with Scanning SWATH and high-flow chromatography

Great advances have been made to quantify proteomes at depth and high precision. However, the inherent complexity of the proteome still creates huge challenges to deal with large sample series and longitudinal experiments. Here we report a data-independent acquisition (DIA) method, Scanning SWATH, and new software algorithms, that combine the advantages of data-dependent and DIA acquisition. Exploiting a continuous movement of the precursor isolation window to assign precursor mass to the MS2 fragment traces, Scanning SWATH increases the precursor identifications of up to 70% compared to conventional DIA methods on 1-5 minute chromatographic gradients. Moreover, we achieve significant acceleration of the mass spectrometric duty cycles, facilitating the generation of quantitative precise proteomes with high-flow (800 µL/min) chromatography and gradients that can be as fast as 30 seconds. We demonstrate the application of ultra-fast proteomics in drug mode-of-action screening. Scanning SWATH proteomes capture the mode-of-action of azoles and statins acting as fungistatic drugs.