Glycoinformatic Platforms for Data Interpretation: An HPLC Perspective

High-throughput and automated HPLC techniques allow for the rapid, detailed structural analysis of complex glycans. These advances have the potential for (i) validating a new generation of biomarkers that relate alterations in glycan processing to disease by mining the glycosylation patterns in a variety of disease types and (ii) for monitoring the production of therapeutic glycoproteins. The wealth of knowledge that can be generated justifies the requirement for databases, analytical tools and search facilities. Recent efforts by international consortia have increased the awareness of the need for glycoinformatics and several resources are now available including a suite of novel applications to assist the interpretation of HPLC data collections.

[1]  Y. Ikeda,et al.  A glycomic approach to the identification and characterization of glycoprotein function in cells transfected with glycosyltransferase genes , 2001, Proteomics.

[2]  Claus-Wilhelm von der Lieth,et al.  GlyNest and CASPER: two independent approaches to estimate 1H and 13C NMR shifts of glycans available through a common web-interface , 2006, Nucleic Acids Res..

[3]  J. Marth,et al.  Mammalian N-glycan branching protects against innate immune self-recognition and inflammation in autoimmune disease pathogenesis. , 2007, Immunity.

[4]  David J. Harvey,et al.  HPLC-based analysis of serum N-glycans on a 96-well plate platform with dedicated database software. , 2008, Analytical biochemistry.

[5]  P. Rudd,et al.  Evaluation of the serum N‐linked glycome for the diagnosis of cancer and chronic inflammation , 2008, Proteomics.

[6]  Kiyoko F. Aoki-Kinoshita,et al.  KEGG as a glycome informatics resource. , 2006, Glycobiology.

[7]  N. Packer,et al.  Small-scale enzymatic digestion of glycoproteins and proteoglycans for analysis of oligosaccharides by LC-MS and FACE gel electrophoresis. , 2009, Methods in molecular biology.

[8]  A. Helenius,et al.  Roles of N-linked glycans in the endoplasmic reticulum. , 2004, Annual review of biochemistry.

[9]  Pauline M Rudd,et al.  Determining the Structure of Oligosaccharides N‐ and O‐Linked to Glycoproteins , 2000, Current protocols in protein science.

[10]  Philip V. Toukach,et al.  Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de , 2007, Nucleic Acids Res..

[11]  Martin Frank,et al.  Glycome-DB.org: a portal for querying across the digital world of carbohydrate sequences. , 2009, Glycobiology.

[12]  R. Dwek,et al.  Detailed glycan analysis of serum glycoproteins of patients with congenital disorders of glycosylation indicates the specific defective glycan processing step and provides an insight into pathogenesis. , 2003, Glycobiology.

[13]  Louise Royle,et al.  Separation‐based Glycoprofiling Approaches using Fluorescent Labels , 2007, Proteomics.

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

[15]  Martin Frank,et al.  GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research. , 2006, Glycobiology.

[16]  Kiyoko F. Aoki-Kinoshita.  An Introduction to Bioinformatics for Glycomics Research , 2008, PLoS Comput. Biol..

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

[18]  D. Harvey.  Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2003–2004 , 2008, Mass spectrometry reviews.

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

[20]  Manfred Wuhrer,et al.  Glycosylation profiling in clinical proteomics: heading for glycan biomarkers , 2007, Expert review of proteomics.

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

[22]  Louise Royle,et al.  Proposal for a standard system for drawing structural diagrams of N‐ and O‐linked carbohydrates and related compounds , 2009, Proteomics.

[23]  Pauline M Rudd,et al.  A strategy to reveal potential glycan markers from serum glycoproteins associated with breast cancer progression. , 2008, Glycobiology.

[24]  S. Hakomori,et al.  Glycosylation defining cancer malignancy: New wine in an old bottle , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[25]  David J Harvey,et al.  Proteomic analysis of glycosylation: structural determination of N- and O-linked glycans by mass spectrometry , 2005, Expert review of proteomics.

[26]  Naoyuki Taniguchi,et al.  Comparison of the methods for profiling glycoprotein glycans--HUPO Human Disease Glycomics/Proteome Initiative multi-institutional study. , 2007, Glycobiology.

[27]  C. Lieth,et al.  GlycoCT-a unifying sequence format for carbohydrates. , 2008, Carbohydrate research.

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

[29]  Raymond A. Dwek,et al.  Glycobiology: Toward Understanding the Function of Sugars. , 1996, Chemical reviews.

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

[31]  J. Esko,et al.  The sweet and sour of cancer: glycans as novel therapeutic targets , 2005, Nature Reviews Cancer.

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

[33]  Matrix-assisted laser desorption/ionization mass spectrometry of carbohydrates and glycoconjugates , 2003 .

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

[35]  Matthew P Campbell,et al.  GlycoExtractor: a web-based interface for high throughput processing of HPLC-glycan data. , 2010, Journal of proteome research.