Software for automated interpretation of mass spectrometry data from glycans and glycopeptides.

The purpose of this review is to provide those interested in glycosylation analysis with the most updated information on the availability of automated tools for MS characterization of N-linked and O-linked glycosylation types. Specifically, this review describes software tools that facilitate elucidation of glycosylation from MS data on the basis of mass alone, as well as software designed to speed the interpretation of glycan and glycopeptide fragmentation from MS/MS data. This review focuses equally on software designed to interpret the composition of released glycans and on tools to characterize N-linked and O-linked glycopeptides. Several websites have been compiled and described that will be helpful to the reader who is interested in further exploring the described tools.

[1]  R. Dwek,et al.  Concepts and principles of O-linked glycosylation. , 1998, Critical reviews in biochemistry and molecular biology.

[2]  A. Levchenko,et al.  The Systems Biology of Glycosylation , 2004, Chembiochem : a European journal of chemical biology.

[3]  Bin Ma,et al.  Complexities and Algorithms for Glycan Sequencing Using Tandem Mass Spectrometry , 2008, J. Bioinform. Comput. Biol..

[4]  David Goldberg,et al.  Automated N-glycopeptide identification using a combination of single- and tandem-MS. , 2007, Journal of proteome research.

[5]  Yehia Mechref,et al.  Enzymatic/chemical release of O-glycans allowing MS analysis at high sensitivity. , 2009, Analytical chemistry.

[6]  J. Paulson,et al.  Glycomics: an integrated systems approach to structure-function relationships of glycans , 2005, Nature Methods.

[7]  R Apweiler,et al.  On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database. , 1999, Biochimica et biophysica acta.

[8]  T. Lefebvre,et al.  Dysregulation of the nutrient/stress sensor O-GlcNAcylation is involved in the etiology of cardiovascular disorders, type-2 diabetes and Alzheimer's disease. , 2010, Biochimica et biophysica acta.

[9]  Alessio Ceroni,et al.  GlycoWorkbench: a tool for the computer-assisted annotation of mass spectra of glycans. , 2008, Journal of proteome research.

[10]  Cathy H. Wu,et al.  The Universal Protein Resource (UniProt): an expanding universe of protein information , 2005, Nucleic Acids Res..

[11]  Radoslav Goldman,et al.  Semi-automated identification of N-Glycopeptides by hydrophilic interaction chromatography, nano-reverse-phase LC-MS/MS, and glycan database search. , 2012, Journal of proteome research.

[12]  O. Lund,et al.  NetOglyc: Prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility , 1998, Glycoconjugate Journal.

[13]  Nicolle H. Packer,et al.  GlycoSuiteDB: a new curated relational database of glycoprotein glycan structures and their biological sources , 2001, Nucleic Acids Res..

[14]  J. Dennis,et al.  Protein glycosylation in development and disease , 1999, BioEssays : news and reviews in molecular, cellular and developmental biology.

[15]  M. Betenbaugh,et al.  Controlling N-linked glycan site occupancy. , 2005, Biochimica et biophysica acta.

[16]  J F Vliegenthart,et al.  New type of linkage between a carbohydrate and a protein: C-glycosylation of a specific tryptophan residue in human RNase Us. , 1994, Biochemistry.

[17]  H. Desaire,et al.  Glycopeptide analysis by mass spectrometry. , 2008, The Analyst.

[18]  Carolyn R. Bertozzi,et al.  Chemical Glycobiology , 2001, Science.

[19]  Sakari Joenväärä,et al.  N-glycoproteomics - an automated workflow approach. , 2008, Glycobiology.

[20]  Petr Novak,et al.  Cysteine S‐glycosylation, a new post‐translational modification found in glycopeptide bacteriocins , 2011, FEBS letters.

[21]  Simon J North,et al.  Mass spectrometry in the analysis of N-linked and O-linked glycans. , 2009, Current opinion in structural biology.

[22]  Haixu Tang,et al.  Automated interpretation of MS/MS spectra of oligosaccharides , 2005, ISMB.

[23]  H. Puschmann,et al.  The C-Glycosylation of Flavonoids in Cereals*♦ , 2009, The Journal of Biological Chemistry.

[24]  E. Go,et al.  GlycoPep DB: a tool for glycopeptide analysis using a "Smart Search". , 2007, Analytical chemistry.

[25]  Hsien-Da Huang,et al.  dbPTM: an information repository of protein post-translational modification , 2005, Nucleic Acids Res..

[26]  Jonathan D. Hirst,et al.  Prediction of glycosylation sites using random forests , 2008, BMC Bioinformatics.

[27]  Ziding Zhang,et al.  Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k-spaced amino acid pairs , 2008, BMC Bioinformatics.

[28]  D. Ashline,et al.  Carbohydrate structural isomers analyzed by sequential mass spectrometry. , 2007, Analytical chemistry.

[29]  Yuliet Mazola,et al.  Integrating Bioinformatics Tools to Handle Glycosylation , 2011, PLoS Comput. Biol..

[30]  R. Tucker.  A spoonful of sugar...? , 2001, The Veterinary record.

[31]  Hongfang Liu,et al.  dbOGAP - An Integrated Bioinformatics Resource for Protein O-GlcNAcylation , 2011, BMC Bioinformatics.

[32]  E. Tian,et al.  Recent insights into the biological roles of mucin-type O-glycosylation , 2009, Glycoconjugate Journal.

[33]  C. Bertozzi,et al.  Glycans in cancer and inflammation — potential for therapeutics and diagnostics , 2005, Nature Reviews Drug Discovery.

[34]  J. Peter-Katalinic,et al.  Software platform for high-throughput glycomics. , 2009, Analytical chemistry.

[35]  Ning Zhang,et al.  UniPep - a database for human N-linked glycosites: a resource for biomarker discovery , 2006, Genome Biology.

[36]  J. Leary,et al.  STAT: a saccharide topology analysis tool used in combination with tandem mass spectrometry. , 2000, Analytical chemistry.

[37]  Martin Frank,et al.  Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB , 2004, Nucleic Acids Res..

[38]  Lutgarde Arckens,et al.  Sweet Substitute: A software tool for in silico fragmentation of peptide‐linked N‐glycans , 2004, Proteomics.

[39]  E. Go,et al.  Simplification of mass spectral analysis of acidic glycopeptides using GlycoPep ID. , 2007, Analytical chemistry.

[40]  Pauline M. Rudd,et al.  GlycoBase and autoGU: tools for HPLC-based glycan analysis , 2008, Bioinform..

[41]  Thomas Wetter,et al.  GlycomeDB – integration of open-access carbohydrate structure databases , 2008, BMC Bioinformatics.

[42]  Sergey Y. Vakhrushev,et al.  SysBioWare : Structure Assignment Tool for Automated Glycomics , 2010 .

[43]  J. Michalski,et al.  The use of mass spectrometry for the proteomic analysis of glycosylation , 2006, Proteomics.

[44]  S Brunak,et al.  Scanning the available Dictyostelium discoideum proteome for O-linked GlcNAc glycosylation sites using neural networks. , 1999, Glycobiology.

[45]  Jian Min Ren,et al.  N-Glycan structure annotation of glycopeptides using a linearized glycan structure database (GlyDB). , 2007, Journal of proteome research.

[46]  Hui Ying Gao.  Generation of asparagine-linked glycan structure databases and their use , 2009, Journal of the American Society for Mass Spectrometry.

[47]  Pauline M Rudd,et al.  A systematic approach to protein glycosylation analysis: a path through the maze. , 2010, Nature chemical biology.

[48]  Carolyn R Bertozzi,et al.  The chemistry and biology of mucin-type O-linked glycosylation. , 2005, Bioorganic & medicinal chemistry.

[49]  N. Blow.  Glycobiology: A spoonful of sugar , 2009, Nature.

[50]  R. Renkonen,et al.  De novo glycan structure search with the CID MS/MS spectra of native N-glycopeptides. , 2009, Glycobiology.

[51]  László Drahos,et al.  GlycoMiner: a new software tool to elucidate glycopeptide composition. , 2008, Rapid communications in mass spectrometry : RCM.

[52]  K. Julenius.  NetCGlyc 1.0: prediction of mammalian C-mannosylation sites. , 2007, Glycobiology.

[53]  Haixu Tang,et al.  Mapping site-specific protein N-glycosylations through liquid chromatography/mass spectrometry and targeted tandem mass spectrometry. , 2010, Rapid communications in mass spectrometry : RCM.

[54]  Vasant Honavar,et al.  Glycosylation site prediction using ensembles of Support Vector Machine classifiers , 2007, BMC Bioinformatics.

[55]  Catherine A. Cooper,et al.  GlycoMod – A software tool for determining glycosylation compositions from mass spectrometric data , 2001, Proteomics.

[56]  T. H. Thanka Christlet,et al.  Database analysis of O-glycosylation sites in proteins. , 2001, Biophysical journal.

[57]  James Paulson,et al.  Automatic annotation of matrix‐assisted laser desorption/ionization N‐glycan spectra , 2005, Proteomics.

[58]  René Ranzinger,et al.  “Glyco‐peakfinder” – de novo composition analysis of glycoconjugates , 2007, Proteomics.

[59]  Ningombam Sanjib Meitei,et al.  Bioinformatics in glycomics: glycan characterization with mass spectrometric data using SimGlycan. , 2010, Methods in molecular biology.

[60]  R. Spiro.  Protein glycosylation: nature, distribution, enzymatic formation, and disease implications of glycopeptide bonds. , 2002, Glycobiology.

[61]  Robert J Chalkley,et al.  Mass Spectrometric Analysis, Automated Identification and Complete Annotation of O-Linked Glycopeptides , 2010, European journal of mass spectrometry.

[62]  Haixu Tang,et al.  A Computational Approach for the Identification of Site-Specific Protein Glycosylations Through Ion-Trap Mass Spectrometry , 2006, Systems Biology and Computational Proteomics.

[63]  M. Tajiri,et al.  Quantitation of saccharide compositions of O-glycans by mass spectrometry of glycopeptides and its application to rheumatoid arthritis. , 2010, Journal of proteome research.

[64]  Daniel Kolarich,et al.  GlycoSpectrumScan: fishing glycopeptides from MS spectra of protease digests of human colostrum sIgA. , 2010, Journal of proteome research.

[65]  Angela M Zivkovic,et al.  Simultaneous and extensive site-specific N- and O-glycosylation analysis in protein mixtures. , 2011, Journal of proteome research.

[66]  David M Rocke,et al.  A new computer program (GlycoX) to determine simultaneously the glycosylation sites and oligosaccharide heterogeneity of glycoproteins. , 2006, Journal of proteome research.

[67]  Jeremy C. Collette,et al.  Emerging Paradigms for the Initiation of Mucin-type Protein O-Glycosylation by the Polypeptide GalNAc Transferase Family of Glycosyltransferases* , 2011, The Journal of Biological Chemistry.

[68]  David Goldberg,et al.  Automatic determination of O-glycan structure from fragmentation spectra. , 2006, Journal of proteome research.

[69]  Claus-Wilhelm von der Lieth,et al.  GlycoFragment and GlycoSearchMS: web tools to support the interpretation of mass spectra of complex carbohydrates , 2004, Nucleic Acids Res..

[70]  H. Desaire,et al.  When can glycopeptides be assigned based solely on high-resolution mass spectrometry data? , 2009 .

[71]  Claus-W von der Lieth,et al.  GLYCO‐FRAGMENT: A web tool to support the interpretation of mass spectra of complex carbohydrates , 2003, Proteomics.

[72]  Haixu Tang,et al.  Improving confidence in detection and characterization of protein N-glycosylation sites and microheterogeneity. , 2011, Rapid communications in mass spectrometry : RCM.

[73]  Hélène Perreault,et al.  Automated structural assignment of derivatized complex N-linked oligosaccharides from tandem mass spectra. , 2002, Rapid communications in mass spectrometry : RCM.

[74]  Lara K Mahal,et al.  New technologies for glycomic analysis: toward a systematic understanding of the glycome. , 2011, Annual review of analytical chemistry.

[75]  David Hua,et al.  GlycoPep grader: a web-based utility for assigning the composition of N-linked glycopeptides. , 2012, Analytical chemistry.

[76]  Richard S. Lee,et al.  Global methods for protein glycosylation analysis by mass spectrometry. , 2006, Biochimica et biophysica acta.

[77]  Nicolle H. Packer,et al.  Mucin‐type O‐glycosylation – putting the pieces together , 2010, The FEBS journal.

[78]  Søren Brunak,et al.  O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins , 1999, Nucleic Acids Res..

[79]  Søren Brunak,et al.  Prediction of Glycosylation Across the Human Proteome and the Correlation to Protein Function , 2001, Pacific Symposium on Biocomputing.