Proteomics 2013, 13, 341–354 341 DOI 10.1002/pmic.201200149 REVIEW Glycobioinformatics: Current strategies and tools for data mining in MS-based glycoproteomics Feng Li 1,2 , Olga V. Glinskii 1,3 and Vladislav V. Glinsky 1,2 1 Research Service, Harry S. Truman Memorial Veterans Hospital, Columbia, MO, USA 2 Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, MO, USA 3 Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, MO, USA Glycobioinformatics is a rapidly developing field providing a vital support for MS-based gly- coproteomics research. Recent advances in MS greatly increased technological capabilities for high throughput glycopeptide analysis. However, interpreting MS output, in terms of iden- tifying glycan structures, attachment sites and glycosylation linkages still presents multiple challenges. Here, we discuss current strategies used in MS-based glycoproteomics and bioin- formatics tools available for MS-based glycopeptide and glycan analysis. We also provide a brief overview of recent efforts in glycobioinformatics such as the new initiative UniCarbKB directed toward developing more comprehensive and unified glycobioinformatics platforms. With regards to glycobioinformatics tools and applications, we do not express our personal preferences or biases, but rather focus on providing a concise description of main features and functionalities of each application with the goal of assisting readers in making their own choices and identifying and locating glycobioinformatics tools most suitable for achieving their experimental objectives. Keywords: Bioinformatics / Glycan analysis / Glycomics / Glycoproteomics / MS Received: April 10, 2012 Revised: October 6, 2012 Accepted: November 6, 2012 PTMs of proteins are the primary means used by prokary- otic and eukaryotic cells to regulate the activity of key pro- teins [1–3]. PTMs may involve both chemical alterations of protein side chains and a cleavage of the main chain peptide bonds. The dynamic modification and diversification enabled by PTMs greatly increases molecular variants of cellular pro- teins by an estimated one or two orders of magnitude over the number encoded by the genome [4]. Therefore, charac- terizing structures, sites, and dynamics of the protein PTMs is essential for understanding their diversity, structure, and function in the “-omics” age [5]. Correspondence: Dr. Vladislav V. Glinsky, M263 Medical Sciences Bldg., Department of Pathology and Anatomical Sciences, Uni- versity of Missouri, Columbia, MO 65212, USA E-mail: glinskiivl@missouri.edu Fax: +1-573-814-6551 Abbreviations: CFG, consortium for functional glycomics; ECD, electron capture dissociation; ETD, electron transfer dissociation; IGAP, intact glycopeptide analysis pipeline 1 Glycosylation: Most abundant and structurally diverse posttranslational modification Covalent attachment of sugars or glycans to proteins or lipids is defined as glycosylation. Glycosylation represents not only the most abundant protein PTM, but also by far the most structurally diverse one [6]. Although monosac- charides do not constitute overly complicated chemical group, 13 different monosaccharides and eight differ- ent amino acids involved in glycoprotein linkages results in a total of at least 41 different glycan-protein bonds. Comprehensive information about various monosaccharide residues can be found in the MonosaccharideDB database (http://www.monosaccharidedb.org), which is being devel- oped as part of the EUROCarbDB and GLYCOSCIENCES.de projects [7]. Furthermore, due to additional modifications on terminal glycans of oligosaccharide branches such as fuco- sylation, sulfation, acetylation, and/or sialylation (about 50 different sialic acids are known), the molecular diversity of Colour Online: See the article online to view Figs. 1–3 in colour. C  2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com