Glycan size and attachment site location affect electron transfer dissociation (ETD) fragmentation and automated glycopeptide identification
Glycan size and attachment site location affect electron transfer dissociation (ETD) fragmentation and automated glycopeptide identification
Abstract We used a small synthetic glycopeptide library to systematically evaluate the effect of glycosylation site location and glycan size on the efficiency of ETD MS/MS fragmentation and subsequent automated identification. Understanding how the physico-chemical properties of glycopeptides influence glycopeptide fragmentation allows for optimizing fragmentation conditions and software assisted data analyses, which rely on informative fragmentation spectra for subsequent data processing to identify glycopeptides. Often, mis-assignment of glycopeptides occurs due to uncertainties such as failure to produce sufficient peptide backbone fragment ions. Our synthetic glycopeptide library contained glycopeptides differing in glycosylation site position within the peptide as well as glycan size (from the pentasaccharide N-glycan core to fully sialylated, biantennary N-glycans). Different software solutions such as SEQUEST and Amanda were compared for ETD glycopeptide identification. We found that all, glycan size, glycosylation site position within a glycopeptide and individual precursor m/z significantly impacted the number and quality of assignable glycopeptide backbone fragments, and thus the likelihood to be correctly identified in software assisted data analyses.
Kolarich Daniel、Hinneburg Hannes、Seeberger Peter H、Alagesan Kathirvel、Var¨?n Silva Daniel
Institute for Glycomics, Griffith University Gold Coast Campus||Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces||ARC Centre for Nanoscale BioPhotonicsInstitute for Glycomics, Griffith University Gold Coast Campus||Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces||Department of Molecular Science, Faculty of Science and Engineering, Macquarie UniversityDepartment of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces||Institute of Chemistry and Biochemistry, Freie Universit?t BerlinInstitute for Glycomics, Griffith University Gold Coast Campus||Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces||Institute of Chemistry and Biochemistry, Freie Universit?t BerlinDepartment of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces
生物科学研究方法、生物科学研究技术生物化学分子生物学
GlycopeptideGlycoproteomicsElectron transfer dissociationETD
Kolarich Daniel,Hinneburg Hannes,Seeberger Peter H,Alagesan Kathirvel,Var¨?n Silva Daniel.Glycan size and attachment site location affect electron transfer dissociation (ETD) fragmentation and automated glycopeptide identification[EB/OL].(2025-03-28)[2025-07-02].https://www.biorxiv.org/content/10.1101/676288.点此复制
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