ArticleAnalytical and bioanalytical chemistry2025
Quantitative proteome-wide O-glycoproteomics analysis with FragPipe.
Article in Analytical and bioanalytical chemistry, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Systematic Quantification of Protein O-GlcNAcylation Reveals Common and Cell-Type-Specific Responses to N-Glycosylation Inhibition in Human Cells.Analytical chemistry · 2026Article
- A New Detailed Mass Offset Search in MSFragger for Improved Interpretation of Complex PTMs.Journal of proteome research · 2026Article
- dELTA-MS: A Mass Spectrometry-Based Proteomics Approach for Identifying ADP-Ribosylation Sites and Forms.Journal of proteome research · 2025Article
- Comparative analysis of glycoproteomic software using a tailored glycan database.Analytical and bioanalytical chemistry · 2025Article
- Recent Advances in Mass Spectrometry-Based Bottom-Up Proteomics.Analytical chemistry · 2025Review
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Authors and funding
7 authors.
Funding
Abstract
Identification of O-glycopeptides from tandem mass spectrometry data is complicated by the near complete dissociation of O-glycans from the peptide during collisional activation and by the combinatorial explosion of possible glycoforms when glycans are retained intact in electron-based activation. The recent O-Pair search method provides an elegant solution to these problems, using a collisional activation scan to identify the peptide sequence and total glycan mass, and a follow-up electron-based activation scan to localize the glycosite(s) using a graph-based algorithm in a reduced search space. Our previous O-glycoproteomics methods with MSFragger-Glyco allowed for extremely fast and sensitive identification of O-glycopeptides from collisional activation data but had limited support for site localization of glycans and quantification of glycopeptides. Here, we report an improved pipeline for O-glycoproteomics analysis that provides proteome-wide, site-specific, quantitative results by incorporating the O-Pair method as a module within FragPipe. In addition to improved search speed and sensitivity, we add flexible options for oxonium ion-based filtering of glycans and support for a variety of MS acquisition methods and provide a comparison between all software tools currently capable of O-glycosite localization in proteome-wide searches.
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Registered trials
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