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- Title
Large-scale identification and visualization of N-glycans with primary structures using GlySeeker.
- Authors
Xiao, Kaijie; Wang, Yue; Shen, Yun; Han, Yuyin; Tian, Zhixin
- Abstract
Rationale: Most of the current popular tandem mass spectrometers have the capability of resolving the primary structures (monosaccharide composition, sequence and linkage) of N-glycans; however, compositions or putative structures have mostly been reported so far. Identification and visualization tools of N-glycans are needed. Methods: The isotopic mass-to-charge ratio and envelope fingerprinting algorithm, which has been successfully used for intact protein database search and identification, was adapted for N-glycan database search, and a stand-alone N-glycan database search engine, GlySeeker, for automated N-glycan identification and visualization was developed and successfully benchmarked. Both pseudo 2D graph and one-line text formats with one-letter symbols for monosaccharides were proposed for representing N-glycans. N-glycans were identified with comprehensive interpretation of product ions and false discovery rate (FDR) control. Results: In a database search of reversed-phase liquid chromatography/tandem mass spectrometry (RPLC/MS/MS) datasets of the N-glycome enriched from OVCAR-3 ovarian cancer cells, with FDR ≤1% and number of best hits (NoBHs) = 1-30, 1525 N-glycans with comprehensive primary structural information (composition, sequence and linkage) were identified and visualized; among these 1525 N-glycans, 559 had NoBHs = 1, i.e. their structures were uniquely identified. This represents a large-scale identification and visualization of N-glycans with primary structures from tandem mass spectra. Conclusions: A stand-alone N-glycan database search engine called GlySeeker has been developed for large-scale identification and visualization of N-glycans with comprehensive interpretation of tandem mass spectra and FDR control.
- Subjects
GLYCANS; MINIMAL sculpture; TANDEM mass spectrometry; MASS-to-charge ratio; FALSE discovery rate
- Publication
Rapid Communications in Mass Spectrometry: RCM, 2018, Vol 32, Issue 2, p142
- ISSN
0951-4198
- Publication type
Article
- DOI
10.1002/rcm.8023