RT Journal Article SR Electronic T1 Deep ubiquitination site profiling by single-shot data-independent acquisition mass spectrometry JF bioRxiv FD Cold Spring Harbor Laboratory SP 2020.07.23.218651 DO 10.1101/2020.07.23.218651 A1 Steger, Martin A1 Ihmor, Phillip A1 Backman, Mattias A1 Müller, Stefan A1 Daub, Henrik YR 2020 UL http://biorxiv.org/content/early/2020/07/24/2020.07.23.218651.abstract AB We report a highly optimized proteomics method for in-depth ubiquitination profiling, which combines efficient protein extraction and data-independent acquisition mass spectrometry (DIA-MS). Employing DIA for both spectral library generation and single-shot sample analysis, we quantify up to 70,000 ubiquitinated peptides per MS run with high precision, data completeness and throughput. Our approach resolves the dynamics of ubiquitination and protein degradation with an unprecedented analytical depth.Competing Interest StatementAll authors are employees of Evotec Muenchen GmbH (Munich, Germany)