Time-resolved in vivo ubiquitinome profiling by DIA-MS reveals USP7 targets on a proteome-wide scale.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
13 09 2021
13 09 2021
Historique:
received:
25
02
2021
accepted:
11
08
2021
entrez:
14
9
2021
pubmed:
15
9
2021
medline:
21
10
2021
Statut:
epublish
Résumé
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)-MS and neural network-based data processing specifically optimized for ubiquitinomics. Compared to data-dependent acquisition (DDA), our method more than triples identification numbers to 70,000 ubiquitinated peptides in single MS runs, while significantly improving robustness and quantification precision. Upon inhibition of the oncology target USP7, we simultaneously record ubiquitination and consequent changes in abundance of more than 8,000 proteins at high temporal resolution. While ubiquitination of hundreds of proteins increases within minutes of USP7 inhibition, we find that only a small fraction of those are ever degraded, thereby dissecting the scope of USP7 action. Our method enables rapid mode-of-action profiling of candidate drugs targeting DUBs or ubiquitin ligases at high precision and throughput.
Identifiants
pubmed: 34518535
doi: 10.1038/s41467-021-25454-1
pii: 10.1038/s41467-021-25454-1
pmc: PMC8438043
doi:
Substances chimiques
Proteome
0
Ubiquitin
0
USP7 protein, human
EC 3.4.19.12
Ubiquitin-Specific Peptidase 7
EC 3.4.19.12
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
5399Informations de copyright
© 2021. The Author(s).
Références
Nat Methods. 2015 Mar;12(3):258-64, 7 p following 264
pubmed: 25599550
Nat Biotechnol. 2008 Dec;26(12):1367-72
pubmed: 19029910
Curr Opin Cell Biol. 2019 Jun;58:85-94
pubmed: 30897496
Mol Cell Proteomics. 2011 Oct;10(10):M111.013284
pubmed: 21890473
Cell Cycle. 2004 Jun;3(6):689-92
pubmed: 15118411
Nat Methods. 2020 Jan;17(1):41-44
pubmed: 31768060
Mol Cell Proteomics. 2014 Sep;13(9):2513-26
pubmed: 24942700
Annu Rev Cell Dev Biol. 2018 Oct 6;34:137-162
pubmed: 30110556
Cell. 2020 Apr 2;181(1):102-114
pubmed: 31955850
Nat Chem Biol. 2018 Feb;14(2):118-125
pubmed: 29200206
Mol Cell Proteomics. 2013 Mar;12(3):825-31
pubmed: 23266961
Nat Cell Biol. 2012 Oct;14(10):1089-98
pubmed: 23000965
Cell. 2021 Feb 4;184(3):844
pubmed: 33545038
Nat Commun. 2020 Feb 7;11(1):787
pubmed: 32034161
Cell Cycle. 2015;14(10):1540-7
pubmed: 25785348
Mol Omics. 2019 Oct 7;15(5):348-360
pubmed: 31465043
Nat Methods. 2017 Sep;14(9):903-908
pubmed: 28783153
Nature. 2017 Oct 26;550(7677):481-486
pubmed: 29045389
Nucleic Acids Res. 2016 Dec 15;44(22):11033
pubmed: 27683222
Nat Biotechnol. 2010 Aug;28(8):868-73
pubmed: 20639865
Mol Cell Proteomics. 2013 Oct;12(10):2992-3005
pubmed: 23792921
Nature. 2004 Oct 14;431(7010):873-8
pubmed: 15386022
Nat Biotechnol. 2021 Jul;39(7):846-854
pubmed: 33767396
Cell Chem Biol. 2019 Feb 21;26(2):156-177
pubmed: 30554913
Nature. 2017 Oct 26;550(7677):534-538
pubmed: 29045385
Trends Immunol. 2020 Apr;41(4):327-340
pubmed: 32139316
Nucleic Acids Res. 2015 Apr 20;43(7):e47
pubmed: 25605792
Nat Methods. 2014 Mar;11(3):319-24
pubmed: 24487582
Science. 2014 Jan 17;343(6168):301-5
pubmed: 24292625
Nat Protoc. 2013 Oct;8(10):1950-60
pubmed: 24051958
Mol Cell Proteomics. 2012 Jun;11(6):O111.016717
pubmed: 22261725
Mol Cell. 2011 Oct 21;44(2):325-40
pubmed: 21906983
Biochem Soc Trans. 2017 Oct 15;45(5):1137-1148
pubmed: 28939693
EMBO J. 2008 Jul 9;27(13):1863-74
pubmed: 18566590
Anal Chem. 2009 Aug 1;81(15):6481-8
pubmed: 19572557
Nat Commun. 2021 Jan 11;12(1):254
pubmed: 33431886
Cell. 2007 Nov 30;131(5):887-900
pubmed: 18001824
Nucleic Acids Res. 2019 Jan 8;47(D1):D529-D541
pubmed: 30476227
Nat Genet. 2012 May;44(5):598-602
pubmed: 22466611
Nat Struct Mol Biol. 2018 Jul;25(7):631-640
pubmed: 29967540
Mol Syst Biol. 2015 Jun 02;11(6):810
pubmed: 26038114
Nat Rev Mol Cell Biol. 2020 Aug;21(8):421-438
pubmed: 32457508
Nat Methods. 2011 May;8(5):430-5
pubmed: 21423193
Nat Methods. 2016 Sep;13(9):731-40
pubmed: 27348712
Cell Death Differ. 2021 Feb;28(2):427-438
pubmed: 33130827
Nat Cell Biol. 2016 May 27;18(6):579-86
pubmed: 27230526
Anal Chem. 2003 Feb 1;75(3):663-70
pubmed: 12585499
J Pathol. 2020 May;251(1):100-112
pubmed: 32154592
Cell. 2011 Oct 14;147(2):459-74
pubmed: 21963094
Nat Methods. 2008 Jun;5(6):459-60
pubmed: 18511913
Cell Chem Biol. 2021 Jan 21;28(1):78-87.e3
pubmed: 33007217
J Proteome Res. 2007 Sep;6(9):3549-57
pubmed: 17676885
Mol Cell. 2015 Sep 17;59(6):956-69
pubmed: 26365382