The DOI matches its Crossref record; 55 of the 55 references it cites were found in a registry or an index.
Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco
Open accessAbstract
Recent advances in methods for enrichment and mass spectrometric analysis of intact glycopeptides have produced large-scale glycoproteomics datasets, but interpreting these data remains challenging. We present MSFragger-Glyco, a glycoproteomics mode of the MSFragger search engine, for fast and sensitive identification of N- and O-linked glycopeptides and open glycan searches. Reanalysis of recent N-glycoproteomics data resulted in annotation of 80% more glycopeptide spectrum matches (glycoPSMs) than previously reported. In published O-glycoproteomics data, our method more than doubled the number of glycoPSMs annotated when searching the same glycans as the original search, and yielded 4- to 6-fold increases when expanding searches to include additional glycan compositions and other modifications. Expanded searches also revealed many sulfated and complex glycans that remained hidden to the original search. With greatly improved spectral annotation, coupled with the speed of index-based scoring, MSFragger-Glyco makes it possible to comprehensively interrogate glycoproteomics data and illuminate the many roles of glycosylation. MSFragger-Glyco allows identification of N- and O-linked glycopeptides using the localization-aware open search strategy of the MSFragger search engine.
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Biopython: freely available python tools for computational molecular biology and bioinformatics
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Self-citationA Statistical Model for Identifying Proteins by Tandem Mass Spectrometry
Nesvizhskii, A. I., Keller, A., Kolker, E., & Aebersold, R. (2003) · Analytical Chemistry · doi:10.1021/ac0341261 · Cited by 4,809
Self-citationVarki, A. (2017) · Glycobiology · doi:10.1093/glycob/cww086 · Cited by 2,635
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics
Kong, A. T., Leprevost, F. V., Avtonomov, D. M., Mellacheruvu, D., & Nesvizhskii, A. I. (2017) · Nature Methods · doi:10.1038/nmeth.4256 · Cited by 2,402
Self-citationProteoWizard: open source software for rapid proteomics tools development
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Unraveling the glycosylated immunopeptidome with HLA-Glyco
Bedran, G., Polasky, D. A., Hsiao, Y., Yu, F., da Veiga Leprevost, F., Alfaro, J. A., Cieslik, M., & Nesvizhskii, A. I. (2023) · Nature Communications · doi:10.1038/s41467-023-39270-2 · Cited by 15
Self-citation(2025) · doi:10.1038/s41467-025-60437-6 · Cited by 13
Improved Peptide Search for Identification of SUMO and Sequence-Based Modifiers, in MaxSBM
Lennartsson, C., Kyriakidou, P., Nielsen, M. L., Olsen, J. V., Cox, J., & Hendriks, I. A. (2026) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2026.101589
Metadata
- Authors
- Polasky, D. A., Yu, F., Teo, G. C., & Nesvizhskii, A. I.
- Venue
- Nature Methods
- Published
- 2020-10-05
- Volume
- 17
- Issue
- 11
- Pages
- 1125-1132
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W3090230755
- Cited by
- 293
- References
- 55
- FWCI
- 9.06
- Type
- journal article
- Language
- en
- Open access
- green
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