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Validation of the curation pipeline of UniCarb-DB: Building a global glycan reference MS/MS repository

Journal article
Authors M. P. Campbell
T. Nguyen-Khuong
Catherine A Hayes
Sarah A. Flowers
K. Alagesan
D. Kolarich
N. H. Packer
Niclas G. Karlsson
Published in Biochimica et Biophysica Acta - Proteins and Proteomics
Volume 1844
Issue 1 PART A
Pages 108-116
ISSN 1570-9639
Publication year 2014
Published at Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology
Pages 108-116
Language en
Links dx.doi.org/10.1016/j.bbapap.2013.04...
Keywords Database, Glycan, Glycobiology, Glycomics, Mass spectrometry, Standards, anion, glycoprotein, oligosaccharide, algorithm, article, controlled study, electrospray mass spectrometry, ion trap mass spectrometry, liquid chromatography, peptide library, priority journal, protein database, protein glycosylation, protein structure, proteomics, reference database, standard, tandem mass spectrometry, UniCarb DB database
Subject categories Biochemistry

Abstract

The UniCarb-DB database is an emerging public glycomics data repository, containing over 500 tandem mass spectra (as of March 2013) of glycans released from glycoproteins. A major challenge in glycomics research is to provide and maintain high-quality datasets that will offer the necessary diversity to support the development of accurate bioinformatics tools for data deposition and analysis. The role of UniCarb-DB, as an archival database, is to provide the glycomics community with open-access to a comprehensive LC MS/MS library of N- and O- linked glycans released from glycoproteins that have been annotated with glycosidic and cross-ring fragmentation ions, retention times, and associated experimental metadata descriptions. Here, we introduce the UniCarb-DB data submission pipeline and its practical application to construct a library of LC-MS/MS glycan standards that forms part of this database. In this context, an independent consortium of three laboratories was established to analyze the same 23 commercially available oligosaccharide standards, all by using graphitized carbon-liquid chromatography (LC) electrospray ionization (ESI) ion trap mass spectrometry in the negative ion mode. A dot product score was calculated for each spectrum in the three sets of data as a measure of the comparability that is necessary for use of such a collection in library-based spectral matching and glycan structural identification. The effects of charge state, de-isotoping and threshold levels on the quality of the input data are shown. The provision of well-characterized oligosaccharide fragmentation data provides the opportunity to identify determinants of specific glycan structures, and will contribute to the confidence level of algorithms that assign glycan structures to experimental MS/MS spectra. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. © 2013 Elsevier B.V.

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