ArticleMolecular & cellular proteomics : MCP2021
Peak Filtering, Peak Annotation, and Wildcard Search for Glycoproteomics.
Article in Molecular & cellular proteomics : MCP, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 45 citations in OpenAlex.
- An Overview of Mass Spectrometry-Based Methods to Analyze Post-Translational Modifications.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Improvements in Glycoproteomics through Architecture Changes to the Orbitrap Tribrid MS Platform.Analytical chemistry · 2025Article
- GNOme, an ontology for glycan naming and subsumption.Analytical and bioanalytical chemistry · 2025Article
- Comparative analysis of glycoproteomic software using a tailored glycan database.Analytical and bioanalytical chemistry · 2025Article
- Recombinant production platform for Group A Streptococcus glycoconjugate vaccines.NPJ vaccines · 2025Article
- Immunoglobulin A carries sulfated andFrontiers in molecular biosciences · 2025Article
- Autonomous Dissociation-type Selection for Glycoproteomics Using a Real-Time Library Search.Journal of proteome research · 2024Article
- A Novel Integrated Pipeline for Site-Specific Quantification of N-glycosylation.Phenomics (Cham, Switzerland) · 2024Article
- Human brain glycoform coregulation network and glycan modification alterations in Alzheimer's disease.Science advances · 2024Article
- Ultrastructural and glycoproteomic characterization of Prevotella intermedia: Insights into O-glycosylation and outer membrane vesicles.MicrobiologyOpen · 2024Article
- Analysis of the Healthy Platelet Proteome Identifies a New Form of Domain-Specific O-Fucosylation.Molecular & cellular proteomics : MCP · 2024Article
- MALDI Peptide Mapping for Fast Analysis in Protein Footprinting.International journal of mass spectrometry · 2023Article
- Characterization of theJournal of bacteriology · 2023Article
- Development and validation of a method for analyzing the sialylated glycopeptides of recombinant erythropoietin in urine using LC-HRMS.Scientific reports · 2023Article
- Recent advances in mass spectrometry analysis of neuropeptides.Mass spectrometry reviews · 2023Review
- Systems-Wide Site-Specific Analysis of Glycoproteins.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Systems-Wide Site-Specific Analysis of Glycoproteins.Methods in molecular biology (Clifton, N.J.) · 2023Article
- DecipheringMolecular omics · 2022Article
- Measuring change in glycoprotein structure.Current opinion in structural biology · 2022Review
- Characterization of the O-Glycoproteome of Porphyromonas gingivalis.Microbiology spectrum · 2022Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Glycopeptides in peptide or digested protein samples pose a number of analytical and bioinformatics challenges beyond those posed by unmodified peptides or peptides with smaller posttranslational modifications. Exact structural elucidation of glycans is generally beyond the capability of a single mass spectrometry experiment, so a reasonable level of identification for tandem mass spectrometry, taken by several glycopeptide software tools, is that of peptide sequence and glycan composition, meaning the number of monosaccharides of each distinct mass, e.g., HexNAc(2)Hex(5) rather than man5. Even at this level, however, glycopeptide analysis poses challenges: finding glycopeptide spectra when they are a tiny fraction of the total spectra; assigning spectra with unanticipated glycans, not in the initial glycan database; and finding, scoring, and labeling diagnostic peaks in tandem mass spectra. Here, we discuss recent improvements to Byonic, a glycoproteomics search program, that address these three issues. Byonic now supports filtering spectra by m/z peaks, so that the user can limit attention to spectra with diagnostic peaks, e.g., at least two out of three of 204.087 for HexNAc, 274.092 for NeuAc (with water loss), and 366.139 for HexNAc-Hex, all within a set mass tolerance, e.g., ± 0.01 Da. Also, new is glycan "wildcard" search, which allows an unspecified mass within a user-set mass range to be applied to N- or O-linked glycans and enables assignment of spectra with unanticipated glycans. Finally, the next release of Byonic supports user-specified peak annotations from user-defined posttranslational modifications. We demonstrate the utility of these new software features by finding previously unrecognized glycopeptides in publicly available data, including glycosylated neuropeptides from rat brain.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.