False-Positive Glycopeptide Identification via In-FAIMS Fragmentation.

Autor: Rangel-Angarita V; Department of Chemistry, Yale University, 275 Prospect Street, New Haven, Connecticut 06511, United States., Mahoney KE; Department of Chemistry, Yale University, 275 Prospect Street, New Haven, Connecticut 06511, United States., Kwon C; Department of Chemistry, Yale University, 275 Prospect Street, New Haven, Connecticut 06511, United States., Sarker R; Department of Chemistry, Yale University, 275 Prospect Street, New Haven, Connecticut 06511, United States., Lucas TM; Department of Chemistry, Yale University, 275 Prospect Street, New Haven, Connecticut 06511, United States., Malaker SA; Department of Chemistry, Yale University, 275 Prospect Street, New Haven, Connecticut 06511, United States.
Jazyk: angličtina
Zdroj: JACS Au [JACS Au] 2023 Sep 12; Vol. 3 (9), pp. 2498-2509. Date of Electronic Publication: 2023 Sep 12 (Print Publication: 2023).
DOI: 10.1021/jacsau.3c00264
Abstrakt: High-field asymmetric waveform ion mobility spectrometry (FAIMS) separates glycopeptides in the gas phase prior to mass spectrometry (MS) analysis, thus offering the potential to analyze glycopeptides without prior enrichment. Several studies have demonstrated the ability of FAIMS to enhance glycopeptide detection but have primarily focused on N-glycosylation. Here, we evaluated FAIMS for O-glycoprotein and mucin-domain glycoprotein analysis using samples of varying complexity. We demonstrated that FAIMS was useful in increasingly complex samples as it allowed for the identification of more glycosylated species. However, during our analyses, we observed a phenomenon called "in FAIMS fragmentation" (IFF) akin to in source fragmentation but occurring during FAIMS separation. FAIMS experiments showed a 2- to 5-fold increase in spectral matches from IFF compared with control experiments. These results were also replicated in previously published data, indicating that this is likely a systemic occurrence when using FAIMS. Our study highlights that although there are potential benefits to using FAIMS separation, caution must be exercised in data analysis because of prevalent IFF, which may limit its applicability in the broader field of O-glycoproteomics.
Competing Interests: The authors declare the following competing financial interest(s): S.A.M. is an inventor on a Stanford patent related to the use of mucinase digestion for glycoproteomic analysis and is a consultant for InterVenn Biosciences.
(© 2023 The Authors. Published by American Chemical Society.)
Databáze: MEDLINE