Dataset Information

Large scale intact glycopeptide identification by Mascot database search

ABSTRACT: We present the adaptability of Mascot search engine for automated identification of intact glycopeptide mass spectra. The steps involved in adopting Mascot for intact glycopeptide analysis include: i) assigning unique one letter codes for monosaccharides, ii) linearizing glycan sequences and iii) preparing custom glycoprotein databases. Stepped normalized collision energy (NCE) for HCD mostly provided both the peptide and glycan information in a single MS2 spectrum. Using standard glycoproteins, we showed that Mascot can be adopted for automated annotation of both N- and O-linked glycopeptides. In a large scale validation study, a total of 257 glycoproteins containing 970 unique glycosylation sites and 3447 non-redundant N-linked glycopeptide variants were identified in serum samples. This represent a single tool that collectively allows the i) elucidation of N- and O-linked glycopeptide spectra, ii) matching glycopeptides to known protein sequences, and iii) high-throughput, batch wise analysis of large scale glycoproteomics data sets.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Bernd Thiede

PROVIDER: MSV000082567 | MassIVE | Mon Jul 02 12:38:00 BST 2018

SECONDARY ACCESSION(S): PXD005931

REPOSITORIES: MassIVE

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Large-scale intact glycopeptide identification by Mascot database search.

Bollineni Ravi Chand RC Koehler Christian Jeffrey CJ Gislefoss Randi Elin RE Anonsen Jan Haug JH Thiede Bernd B

Scientific reports 20180201 1

Workflows capable of determining glycopeptides in large-scale are missing in the field of glycoproteomics. We present an approach for automated annotation of intact glycopeptide mass spectra. The steps in adopting the Mascot search engine for intact glycopeptide analysis included: (i) assigning one letter codes for monosaccharides, (ii) linearizing glycan sequences and (iii) preparing custom glycoprotein databases. Automated annotation of both N- and O-linked glycopeptides was proven using stand ...[more]

PMID: 29391424

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