A basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology.
Bioinformatic analysis
High-resolution mass spectrometry technology
Phosphoproteomics
Systems biology
Systems medicine
Journal
Biophysics reports
ISSN: 2364-3420
Titre abrégé: Biophys Rep
Pays: China
ID NLM: 101676603
Informations de publication
Date de publication:
30 Apr 2023
30 Apr 2023
Historique:
received:
09
04
2023
accepted:
28
04
2023
medline:
27
9
2023
pubmed:
27
9
2023
entrez:
27
9
2023
Statut:
ppublish
Résumé
Phosphorylation is one of the most important post-translational modifications (PTMs) of proteins, governing critical protein functions. Most human proteins have been shown to undergo phosphorylation, and phosphoproteomic studies have been widely applied due to recent advancements in high-resolution mass spectrometry technology. Although the experimental workflow for phosphoproteomics has been well-established, it would be useful to optimize and summarize a detailed, feasible protocol that combines phosphoproteomics and data-independent acquisition (DIA), along with follow-up data analysis procedures due to the recent instrumental and bioinformatic advances in measuring and understanding tens of thousands of site-specific phosphorylation events in a single experiment. Here, we describe an optimized Phos-DIA protocol, from sample preparation to bioinformatic analysis, along with practical considerations and experimental configurations for each step. The protocol is designed to be robust and applicable for both small-scale phosphoproteomic analysis and large-scale quantification of hundreds of samples for studies in systems biology and systems medicine.
Identifiants
pubmed: 37753060
doi: 10.52601/bpr.2023.230007
pii: br-9-2-82
pmc: PMC10518521
doi:
Types de publication
Journal Article
Langues
eng
Pagination
82-98Informations de copyright
© The Author(s) 2023.
Déclaration de conflit d'intérêts
Yi Di, Wenxue Li, Barbora Salovska, Qian Ba, Zhenyi Hu, Shisheng Wang and Yansheng Liu declare that they have no conflict of interest.
Références
Cell Rep. 2013 Feb 21;3(2):552-66
pubmed: 23375375
Nat Biotechnol. 2019 Mar;37(3):314-322
pubmed: 30778230
Proteomics. 2023 Feb;23(3-4):e2100387
pubmed: 36422574
Nucleic Acids Res. 2020 Aug 20;48(14):e83
pubmed: 32526036
Nat Methods. 2004 Oct;1(1):39-45
pubmed: 15782151
Proc Natl Acad Sci U S A. 1986 Jul;83(13):4913-7
pubmed: 3088567
Proteomics. 2023 Feb;23(3-4):e2200068
pubmed: 35580145
Nature. 2011 May 19;473(7347):337-42
pubmed: 21593866
Nat Methods. 2016 May;13(5):431-4
pubmed: 27018578
Cell Rep. 2021 Feb 23;34(8):108771
pubmed: 33626354
Mol Cell Proteomics. 2019 Mar;18(3):576-593
pubmed: 30563849
Nat Commun. 2020 Feb 7;11(1):787
pubmed: 32034161
Mol Syst Biol. 2021 Mar;17(3):e9923
pubmed: 33749993
Nucleic Acids Res. 2019 Jan 8;47(D1):D433-D441
pubmed: 30445427
Nat Biotechnol. 2020 Mar;38(3):365-373
pubmed: 31819260
Nat Methods. 2018 Mar;15(3):187-190
pubmed: 29377012
Cell. 2007 Dec 14;131(6):1190-203
pubmed: 18083107
Trends Endocrinol Metab. 2015 Dec;26(12):676-687
pubmed: 26498855
Bioinformatics. 2006 May 1;22(9):1096-102
pubmed: 16481333
Nat Methods. 2015 Mar;12(3):258-64, 7 p following 264
pubmed: 25599550
Dev Cell. 2021 Jan 11;56(1):111-124.e6
pubmed: 33238149
Nat Methods. 2018 May;15(5):371-378
pubmed: 29608554
Nat Commun. 2017 Aug 21;8(1):291
pubmed: 28827567
Nature. 2001 May 17;411(6835):355-65
pubmed: 11357143
Science. 2015 Mar 6;347(6226):1259038
pubmed: 25745177
Mol Cell Proteomics. 2015 May;14(5):1400-10
pubmed: 25724911
Nat Methods. 2013 Aug;10(8):744-6
pubmed: 23793237
Mol Cell Proteomics. 2012 Jun;11(6):O111.016717
pubmed: 22261725
Proteomics. 2019 Dec;19(23):e1900245
pubmed: 31622013
Cell. 2016 Apr 21;165(3):535-50
pubmed: 27104977
Nat Methods. 2019 Sep;16(9):894-901
pubmed: 31384043
J Proteome Res. 2021 Apr 2;20(4):2138-2144
pubmed: 33682416
BMC Bioinformatics. 2012;13 Suppl 16:S12
pubmed: 23176165
Curr Opin Chem Biol. 2004 Feb;8(1):33-41
pubmed: 15036154
Mass Spectrom Rev. 2021 Jul;40(4):309-333
pubmed: 32491218
Mol Cell Proteomics. 2019 Jun;18(6):1242-1254
pubmed: 30948622
Methods Mol Biol. 2018;1711:133-148
pubmed: 29344888
Mol Syst Biol. 2020 Mar;16(3):e9170
pubmed: 32175694
Biochem J. 2001 Aug 1;357(Pt 3):759-67
pubmed: 11463346
J Proteomics. 2022 Jan 6;250:104386
pubmed: 34600153
Nat Methods. 2018 Jun;15(6):440-448
pubmed: 29735998
Sci Adv. 2022 Sep 9;8(36):eabn0756
pubmed: 36083897
Mol Omics. 2021 Jun 14;17(3):413-425
pubmed: 33728422
Cell. 2006 Nov 3;127(3):635-48
pubmed: 17081983
Sci Signal. 2019 Jan 22;12(565):
pubmed: 30670635
Nat Methods. 2020 Jan;17(1):41-44
pubmed: 31768060
Anal Chem. 2021 Feb 16;93(6):3103-3111
pubmed: 33533601
Mol Cell Proteomics. 2017 Dec;16(12):2296-2309
pubmed: 29070702
PLoS Comput Biol. 2017 Mar 27;13(3):e1005462
pubmed: 28346509
Nat Methods. 2016 Sep;13(9):731-40
pubmed: 27348712
Proteomics. 2022 Feb;22(4):e2100316
pubmed: 34878717
Nat Biotechnol. 2017 Aug;35(8):781-788
pubmed: 28604659
Nature. 2016 Sep 14;537(7620):347-55
pubmed: 27629641
Dev Cell. 2018 Oct 22;47(2):205-221.e7
pubmed: 30352176
Nat Cell Biol. 2002 May;4(5):E127-30
pubmed: 11988757
PLoS Comput Biol. 2015 Aug 07;11(8):e1004403
pubmed: 26252020
Clin Transl Med. 2023 Feb;13(2):e1179
pubmed: 36781298
Mol Syst Biol. 2015 Feb 04;11(1):786
pubmed: 25652787
Cell Metab. 2015 Nov 3;22(5):922-35
pubmed: 26437602
Nat Methods. 2016 Nov 29;13(12):966-967
pubmed: 27898060