Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection.
deep proteomics
direct RNA sequencing
long-read RNA sequence
open search
Journal
Journal of proteome research
ISSN: 1535-3907
Titre abrégé: J Proteome Res
Pays: United States
ID NLM: 101128775
Informations de publication
Date de publication:
04 06 2021
04 06 2021
Historique:
pubmed:
18
5
2021
medline:
22
6
2021
entrez:
17
5
2021
Statut:
ppublish
Résumé
Discovery of variant peptides such as a single amino acid variant (SAAV) in shotgun proteomics data is essential for personalized proteomics. Both the resolution of shotgun proteomics methods and the search engines have improved dramatically, allowing for confident identification of SAAV peptides. However, it is not yet known if these methods are truly successful in accurately identifying SAAV peptides without prior genomic information in the search database. We studied this in unprecedented detail by exploiting publicly available long-read RNA sequences and shotgun proteomics data from the gold standard reference cell line NA12878. Searching spectra from this cell line with the state-of-the-art open modification search engine
Identifiants
pubmed: 33998808
doi: 10.1021/acs.jproteome.1c00264
pmc: PMC8280751
doi:
Substances chimiques
Amino Acids
0
Proteome
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
3353-3364Références
Nat Methods. 2019 Dec;16(12):1297-1305
pubmed: 31740818
J Proteome Res. 2021 Apr 2;20(4):1826-1834
pubmed: 32967423
Nat Commun. 2020 Aug 13;11(1):4065
pubmed: 32792501
J Proteome Res. 2020 Jun 5;19(6):2511-2515
pubmed: 32338005
J Proteome Res. 2018 Oct 5;17(10):3606-3612
pubmed: 30141943
Nature. 2008 Nov 27;456(7221):470-6
pubmed: 18978772
J Proteome Res. 2018 Nov 2;17(11):3914-3922
pubmed: 30300549
Clin Biochem. 2019 Apr;66:63-75
pubmed: 30684468
Nature. 2013 Jul 4;499(7456):79-82
pubmed: 23676674
Nat Methods. 2019 Jan;16(1):63-66
pubmed: 30573815
J Proteome Res. 2010 Apr 5;9(4):1716-26
pubmed: 20131910
J Proteome Res. 2014 Jan 3;13(1):241-8
pubmed: 24237036
Bioinformatics. 2015 Jun 15;31(12):i106-15
pubmed: 26072472
Anal Chem. 2000 Feb 15;72(4):757-63
pubmed: 10701260
Proc Natl Acad Sci U S A. 2017 Aug 1;114(31):8247-8252
pubmed: 28720701
Bioinformatics. 2012 Jul 15;28(14):1919-20
pubmed: 22576172
Nature. 2016 May 25;534(7605):55-62
pubmed: 27251275
Mol Syst Biol. 2019 Feb 18;15(2):e8503
pubmed: 30777892
Nucleic Acids Res. 2017 Jan 4;45(D1):D827-D832
pubmed: 27903894
Nat Biotechnol. 2018 Oct 08;:
pubmed: 30295672
J Proteome Res. 2013 Aug 2;12(8):3642-51
pubmed: 23795892
Nat Methods. 2017 Jun 29;14(7):643-644
pubmed: 28661493
J Proteome Res. 2016 Jul 1;15(7):2309-20
pubmed: 27225868
J Proteome Res. 2012 Nov 2;11(11):5221-34
pubmed: 23025403
BMC Bioinformatics. 2016 Jun 17;17(1):244
pubmed: 27316337
Mol Cell Proteomics. 2011 May;10(5):M110.006536
pubmed: 21389108
Nat Biotechnol. 2008 Dec;26(12):1367-72
pubmed: 19029910
Cell. 2016 Jul 28;166(3):755-765
pubmed: 27372738
Expert Rev Proteomics. 2016;13(3):297-308
pubmed: 26697917
Proteomics. 2020 Nov;20(21-22):e1900351
pubmed: 32267083
Bioinformatics. 2020 Feb 15;36(4):1311-1313
pubmed: 31539018
BMC Genomics. 2019 Jan 17;20(1):56
pubmed: 30654742
Genome Res. 2019 Mar;29(3):485-493
pubmed: 30610011
J Proteome Res. 2011 Feb 4;10(2):637-45
pubmed: 21126025
J Mol Cell Biol. 2011 Oct;3(5):309-15
pubmed: 22028381
Mol Cell Proteomics. 2016 Mar;15(3):1060-71
pubmed: 26631509
Mol Cell Proteomics. 2013 Aug;12(8):2341-53
pubmed: 23629695
J Bioinform Comput Biol. 2005 Jun;3(3):697-716
pubmed: 16108090
Nat Methods. 2021 Nov;18(11):1363-1369
pubmed: 34711972
Bioinformatics. 2019 Dec 15;35(24):5243-5248
pubmed: 31077310
Bioinformatics. 2013 Dec 15;29(24):3235-7
pubmed: 24058055
J Proteome Res. 2014 Dec 5;13(12):6058-66
pubmed: 25393578
J Am Soc Mass Spectrom. 2013 Feb;24(2):301-4
pubmed: 23292976
Nat Methods. 2015 Jul;12(7):605-8
pubmed: 26125591
J Proteome Res. 2017 Dec 1;16(12):4425-4434
pubmed: 28965411
J Proteome Res. 2020 Apr 3;19(4):1635-1646
pubmed: 32058723
Mol Cell Proteomics. 2005 Jul;4(7):1002-8
pubmed: 15863400
Proteomics. 2012 May;12(9):1319-27
pubmed: 22589181
J Proteome Res. 2018 Sep 7;17(9):2937-2952
pubmed: 30088773
J Proteome Res. 2015 Feb 6;14(2):778-86
pubmed: 25399873
Nature. 2014 Sep 18;513(7518):382-7
pubmed: 25043054
Nucleic Acids Res. 2019 Jul 2;47(W1):W295-W299
pubmed: 31028400
Methods Mol Biol. 2017;1550:339-368
pubmed: 28188540
J Proteome Res. 2018 Oct 5;17(10):3463-3474
pubmed: 30184435
J Proteome Res. 2012 Feb 3;11(2):1009-17
pubmed: 22103967
Anal Chem. 2005 Jul 15;77(14):4626-39
pubmed: 16013882
J Proteome Res. 2008 Sep;7(9):3838-46
pubmed: 18630943
Nat Commun. 2019 Jun 7;10(1):2524
pubmed: 31175306
J Proteomics. 2010 Oct 10;73(11):2092-123
pubmed: 20816881
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Clin Chem Lab Med. 2017 Aug 28;55(9):1291-1304
pubmed: 28157690
Oncotarget. 2017 Sep 27;8(56):95841-95852
pubmed: 29221171
Nat Biotechnol. 2019 Apr;37(4):469-479
pubmed: 30936560
Front Pharmacol. 2019 Dec 10;10:1484
pubmed: 31920667