PT - JOURNAL ARTICLE AU - Steger, Martin AU - Ihmor, Phillip AU - Backman, Mattias AU - Müller, Stefan AU - Daub, Henrik TI - Deep ubiquitination site profiling by single-shot data-independent acquisition mass spectrometry AID - 10.1101/2020.07.23.218651 DP - 2020 Jan 01 TA - bioRxiv PG - 2020.07.23.218651 4099 - http://biorxiv.org/content/early/2020/07/24/2020.07.23.218651.short 4100 - http://biorxiv.org/content/early/2020/07/24/2020.07.23.218651.full 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)