Ultra-deep and time-resolved in vivo ubiquitinome profiling by DIA-MS reveals USP7 targets on a proteome-wide scale

ABSTRACT: By simultaneously capturing thousands of ubiquitination sites, mass spectrometry (MS)-based ubiquitinomics provides system-level understanding of ubiquitin signaling. Here we present a scalable workflow for deep and precise in vivo ubiquitinome profiling, coupling an improved sample preparation protocol with data-independent acquisition (DIA) mass spectrometry and neural network-based data processing, specifically optimized for ubiquitinomics. Compared to data-dependent acquisition (DDA), our method more than triples the number of quantified ubiquitinated peptides, to 70,000 identifications in single LC-MS runs. At the same time, it significantly improves robustness and quantification precision, thus for the first time enabling large-scale ubiquitinomics screens. We further report a novel strategy for capturing targets of deubiquitinases (DUBs), by simultaneously recording the dynamics of the ubiquitinome and the proteome and at high temporal resolution upon enzyme inhibition. Applying it to the anticancer target USP7, we accurately time ubiquitination and consequent changes in abundance of more than 8,000 proteins, thereby mapping novel putative USP7 targets. We show a strikingly fast modulation of the ubiquitinome when inhibiting USP7 and discover hundreds of ubiquitination sites that are regulated within minutes. Yet only a small fraction of those are degraded, thus dissecting the degradative and non-degradative scope of USP7 action. Mapping the impact of different USP7 inhibitors on the ubiquitinome, we observe substantial overlap of their signatures, but also marked differences. Our method enables for the first time to rapidly profile the mode-of-action of candidate drugs targeting DUBs or ubiquitin ligases at an unprecedented depth.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): T Cell, Colon

DISEASE(S): Colon Cancer

SUBMITTER: Martin Steger  

LAB HEAD: Martin Steger

PROVIDER: PXD023889 | Pride | 2021-08-06

REPOSITORIES: Pride