Detecting diagnostic features in MS/MS spectra of post-translationally modified peptides.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
12 07 2023
12 07 2023
Historique:
received:
04
09
2022
accepted:
23
06
2023
medline:
14
7
2023
pubmed:
13
7
2023
entrez:
12
7
2023
Statut:
epublish
Résumé
Post-translational modifications are an area of great interest in mass spectrometry-based proteomics, with a surge in methods to detect them in recent years. However, post-translational modifications can introduce complexity into proteomics searches by fragmenting in unexpected ways, ultimately hindering the detection of modified peptides. To address these deficiencies, we present a fully automated method to find diagnostic spectral features for any modification. The features can be incorporated into proteomics search engines to improve modified peptide recovery and localization. We show the utility of this approach by interrogating fragmentation patterns for a cysteine-reactive chemoproteomic probe, RNA-crosslinked peptides, sialic acid-containing glycopeptides, and ADP-ribosylated peptides. We also analyze the interactions between a diagnostic ion's intensity and its statistical properties. This method has been incorporated into the open-search annotation tool PTM-Shepherd and the FragPipe computational platform.
Identifiants
pubmed: 37438360
doi: 10.1038/s41467-023-39828-0
pii: 10.1038/s41467-023-39828-0
pmc: PMC10338467
doi:
Substances chimiques
Peptides
0
Glycopeptides
0
Cysteine
K848JZ4886
N-Acetylneuraminic Acid
GZP2782OP0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4132Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM094231
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM135504
Pays : United States
Organisme : NCI NIH HHS
ID : T32 CA140044
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA271037
Pays : United States
Informations de copyright
© 2023. The Author(s).
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