Glycomics : methods and protocols

Section I: Glycan Analysis Subsection A: Released Glycans 1. Analysis of N- and O-Linked Glycans from Glycoproteins Using Maldi-TOF Mass Spectrometry Willy Morelle, Valegh Faid, Frederic Chirat, and Jean-Claude Michalski 2. Infrared Multiphoton Dissociation (IRMPD) Mass Spectrometry for Structural Elucidation of Oligosaccharides Bensheng Li, Hyun Joo An, Jerry L. Hedrick, and Carlito B. Lebrilla 3. Mass Spectrometry of N-linked Glycans Parastoo Azadi and Christian Heiss 4. Solid-phase Permethylation for Glycomic Analysis Yehia Mechref, Pilsoo Kang, and Milos V. Novotny 5. Method for Investigation of Oligosaccharides Using Phenylhydrazine Derivatization Erika Lattova and Helene Perreault 6. 2-Dimensional HPLC Separation with Reverse Phase-Nano-LC-MS/MS for the Characterization of Glycan Pools after Labeling with 2-Aminobenzamide Manfred Wuhrer, Carolien A. M. Koeleman, and Andre M. Deelder 7. Capillary Lectin-Affinity Electrophoresis for Glycan Analysis Kazuaki Kakehi and Mitsuhiro Kinoshita 8. Analysis of Methylated O-Glycan Alditols by CAD-ESI Mass Spectrometry Franz-Georg Hanisch and Stefan Muller 9. High-Throughput and High-Sensitivity Nano-LC/MS and MS/MS for O-Glycan Profiling Hasse Karlsson, Jessica M. Holmen Larsson, Kristina A. Thomsson, Iris Hard, Malin Backstroem, and Gunnar C. Hansson 10. Collision Induced Dissociation Tandem Mass Spectrometry for Structural Elucidation of Glycans Bensheng Li, Hyun Joo An, Jerry L. Hedrick, and Carlito B. Lebrilla 11. The Structural Elucidation of Glycosaminoglycans Vikas Prabhakar, Ishan Capila, and Ram Sasisekharan 12. Labelling Heparan Sulphate Saccharides with Chromophore, Fluorescenceand Mass Tags for HPLC and MS Separations Mark Skidmore, Abdel Atrih, Ed Yates, and Jeremy E. Turnbull 13. Small-Scale Enzymatic Digestion of Glycoproteins and Proteoglycans for Analysis of Oligosaccharides by LC-MS and FACE Gel Electrophoresis Ruby P. Estrella, John M. Whitelock, Rebecca H. Roubin, Nicolle H. Packer, and Niclas G. Karlsson Subsection B: Glycopeptides 14. Enrichment Strategies for Glycopeptides Shigeyasu Ito, Ko Hayama, and Jun Hirabayashi 15. Introductory Glycosylation Analysis Using SDS-PAGE and Peptide Mass Fingerprinting Nicole Wilson, Raina Simpson, and Catherine Cooper-Liddell 16. Characterization of N-Linked Glycosylation on Recombinant Glycoproteins Produced in Pichia pastoris Using ESI-MS and MALDI-TOF Bing Gong, Michael Cukan, Richard Fisher, Huijuan Li, Terrance A. Stadheim, and Tillman Gerngross 17. N-Glycosylation Site Analysis of Human Platelet Proteins by Hydrazide Affinity Capturing and LC-MS/MS Urs Lewandrowski and Albert Sickmann 18. LC/MSn For Glycoprotein Analysis: N-Linked Glycosylation Analysis And Peptide Sequencing Of Glycopeptides Nana Kawasaki, Satsuki Itoh, and Teruhide Yamaguchi Subsection C: O-GlcNAcomics 19. Detecting the 'O-GlcNAc-ome' Detection, Purification, and Analysis of O-GlcNAc Modified Proteins Natasha E. Zachara Subsection D: Glycobioinformatic Tools 20. Preparation of a Glycan Library Using a Variety of Glycosyltrasferases Hiromi Ito, Akihiko Kameyama, Takashi Sato, and Hisashi Narimatsu 21. Data Mining the PDB for Glyco-Related Data Thomas Lutteke and Claus-W. von der Lieth Section II: Carbohydrate-Protein