Proteomics

Dataset Information

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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 (human)

TISSUE(S): Blood Serum

DISEASE(S): Prostate Adenocarcinoma

SUBMITTER: Ravi Chand Bollineni  

LAB HEAD: Bernd Thiede

PROVIDER: PXD005931 | Pride | 2018-02-08

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
Glycoproteins.fasta Fasta
Janus_MascotSearch.dat Other
Janus_Peaklists.mgf Mgf
Janus_Protein_GlycoPeptide_Distiller.rov Other
RB_161031_Aplha1acid_HCD_15.dat Other
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Publications

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]

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