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J Proteome Res. 2016 Nov 4;15(11):4116-4125. Epub 2016 Sep 14.

gFinder: A Web-Based Bioinformatics Tool for the Analysis of N-Glycopeptides.

Author information

1
Graduate Program in Functional Genomics, College of Life Sciences and Biotechnology, Yonsei University , Seoul 03722, Korea.
2
Yonsei Proteome Research Center , Seoul 03722, Korea.
3
Korea Basic Science Institute , Ochang 28199, Chungbuk, Korea.

Abstract

Glycoproteins influence numerous indispensable biological functions, and changes in protein glycosylation have been observed in various diseases. The identification and characterization of glycoprotein and glycosylation sites by mass spectrometry (MS) remain challenging tasks, and great efforts have been devoted to the development of proteome informatics tools that facilitate the MS analysis of glycans and glycopeptides. Here we report on the development of gFinder, a web-based bioinformatics tool that analyzes mixtures of native N-glycopeptides that have been profiled by tandem MS. gFinder not only enables the simultaneous integration of collision-induced dissociation (CID) and high-energy collisional dissociation (HCD) fragmentation but also merges the spectra for high-throughput analysis. These merged spectra expedite the identification of both glycans and N-glycopeptide backbones in tandem MS data using the glycan database and a proteomic search tool (e.g., Mascot). These data can be used to simultaneously characterize peptide backbone sequences and possible N-glycan structures using assigned scores. gFinder also provides many convenient functions that make it easy to perform manual calculations while viewing the spectrum on-screen. We used gFinder to detect an additional protein (Q8N9B8) that was missed from the previously published data set containing N-linked glycosylation. For N-glycan analysis, we used the GlycomeDB glycan structure database, which integrates the structural and taxonomic data from all of the major carbohydrate databases available in the public domain. Thus, gFinder is a convenient, high-throughput analytical tool for interpreting the tandem mass spectra of N-glycopeptides, which can then be used for identification of potential missing proteins having glycans. gFinder is available publicly at http://gFinder.proteomix.org/ .

KEYWORDS:

C-HPP; N-glycan; bioinformatics; chromosome-centric human proteome project; glycoprotein; mass spectrometry

PMID:
27573070
DOI:
10.1021/acs.jproteome.6b00772
[Indexed for MEDLINE]

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