Glycomic Mass Spectrometric Analysis and Data Interpretation Tools

Bioinformatics for Glycobiology and Glycomics: An Introduction

Volumn , Issue , 2009, Pages 223-256

  Karlsson, Niclas G ^a   Packer, Nicolle H ^b  

^a NATIONAL UNIVERSITY OF IRELAND   (Ireland)

^b MACQUARIE UNIVERSITY   (Australia)

Author keywords

Glycobioinformatics; Glycobiology; Glycopeptides; Glycosylation; Mass spectrometry; Oligosaccharides

Indexed keywords

EID: 84862668247     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470029619.ch12     Document Type: Chapter

References (70)

1. Zaia J: Mass spectrometry of oligosaccharides. Mass Spectrom Rev 2004, 23:161-227.
2. Mechref Y, Novotny M: Structural investigations of glycoconjugates at high sensitivity. Chem Rev 2002, 102:321-369.
3. Stellner K, Saito H, Hakomori S: Determination of aminosugar linkages in glycolipids by methylation. Arch Biochem Biophys 1973, 155:464-472.
4. Peter-Katalinic J: Analysis of glycoconjugates by fast atom bombardment mass spectrometry and related MS techniques. Mass Spectrom Rev 1994, 13:77-98.
5. Domon B, Costello C:Asystematic nomenclature of carbohydrate fragmentation in FAB-MS/MS spectra of glycoconjugates. Glycoconj J 1988, 5:397-409.
6. Karlsson N, Karlsson H, Hansson G: Sulphated mucin oligosaccharides from porcine small intestine analyzed by four-sector tandem mass spectrometry. JMass Spectrom 1996, 31:560-572.
7. Wilson N, KarlssonN, Packer N: In SeparationMethods In Proteomics (eds SmejkalGB, Lazarev A). New York: Marcel Dekker; Ch. 19, pp. 345-359.
8. ZhangH, LiX,Martin D, AebersoldR: Identification and quantification ofN-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat Biotechnol 2003, 21:660-666.
9. Kaji H, Saito H, Yamauchi Y, Shinkawa T, Taoka M, Hirabayashi J, Kasai K, Takahashi N, Isobe T: Lectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins. Nat Biotechnol 2003, 21:667-672.
10. Yuan J, Hashii N, Kawasaki N, Itoh S, Kawanishi T, Hayakawa T: Isotope tag method for quantitative analysis of carbohydrates by liquid chromatography-mass spectrometry. J Chromatogr A 2005, 1067:145-152.
11. Xie Y, Liu J, Zhang J, Hedrick J, Lebrilla C: Method for the comparative glycomic analyses of O-linked, mucin-type oligosaccharides. Anal Chem 2004, 76:5186-5197.
12. Ninonuevo M, An H, Yin H, Killeen K, Grimm R, Ward R, German B, Lebrilla C: Nanoliquid chromatography-mass spectrometry of oligosaccharides employing graphitized carbon chromatography on microchip with a high-accuracy mass analyzer. Electrophoresis 2005, 26:3641-3649.
13. Karlsson N, Wilson N, Wirth H, Dawes P, Joshi H, Packer N: Negative ion graphitised carbon nano-liquid chromatography/mass spectrometry increases sensitivity for glycoprotein oligosaccharide analysis. Rapid Commun Mass Spectrom 2004, 18:2282-2292.
14. Kawasaki N, Itoh S, Ohta M, Hayakawa T: Microanalysis of N-linked oligosaccharides in a glycoprotein by capillary liquid chromatography/mass spectrometry and liquid chromatography/ tandem mass spectrometry. Anal Biochem 2003, 316:15-22.
15. Thomsson K, Karlsson H, Hansson G: Sequencing of sulfated oligosaccharides from mucins by liquid chromatography and electrospray ionization tandem mass spectrometry. Anal Chem 2000, 72:4543-4549.
16. Wuhrer M, Koeleman C, Deelder A, Hokke C: Normal-phase nanoscale liquid chromatographymass spectrometry of underivatized oligosaccharides at low-femtomole sensitivity. Anal Chem 2004, 76:833-838.
17. Packer N, Lawson M, Jardine D, Redmond J: A general approach to desalting oligosaccharides released from glycoproteins. Glycoconj J 1998, 15:737-747.
18. Papac D, Briggs J, Chin E, Jones A: A high-throughput microscale method to release N-linked oligosaccharides from glycoproteins formatrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis. Glycobiology 1998, 8:445-454.
19. Küster B, Wheeler S, Hunter A, Dwek R, Harvey D: Sequencing of N-linked oligosaccharides directly from protein gels: in-gel deglycosylation followed by matrix-assisted laser desorption/ ionization mass spectrometry and normal-phase high performance liquid chromatography. Anal Biochem 1997, 250:82-101.
20. Carlson D: Oligosaccharides isolated from pig submaxillary mucin. J Biol Chem 1966, 241:2984-2986.
21. Küster B, Hunter A, Wheeler S, Dwek R, Harvey D: Structural determination of N-linked carbohydrates by matrix-assisted laser desorption/ionization-mass spectrometry following enzymatic release within sodium dodecyl sulfate-polyacrylamide electrophoresis gels: application to species-specific glycosylation of alpha1-acid glycoprotein. Electrophoresis 1998, 19:1950-1959.
22. Wilson N, Schulz B, Karlsson N, Packer N: Sequential analysis of N-and O-linked glycosylation of 2D-PAGE separated glycoproteins. Proteome Res 2002, 1:521-529.
23. KuiW, Easton R, PanicoM, Sutton-Smith M, Morrison J, Lattanzio F, Morris H, Clark G, Dell A, Patankar M: CA125 characterization of the oligosaccharides associated with the human ovarian tumor marker. J Biol Chem 2003, 278:28619-28634.
24. Manna P, Joshi L, Reinhold V, Aubert M, Suganuma N, Pettersson K, Huhtaniemi I: Synthesis, purification and structural and functional characterization of recombinant form of a common genetic variant of human luteinizing hormone. Hum Mol Genet 2002, 11:301-315.
25. Suzuki S, Honda S: Analysis of carbohydrates by capillary electrochromatography. Chromatography 2001, 22:171-179.
26. Handa S, Nakamura K: Modification of sialic acid carboxyl group of ganglioside. J Biochem (Tokyo) 1984, 95:1323-1329.
27. Powell A, Harvey D: Stabilization of sialic acids in N-linked oligosaccharides and gangliosides for analysis by positive ion matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 1996, 10:1027-1032.
28. Harvey D: Fragmentation of negative ions from carbohydrates: Part 3. Fragmentation of hybrid and complex N-linked glycans. J Am Soc Mass Spectrom 2005, 16:647-659.
29. Kobata A, Takasaki S: In Glycobiology (ed. Fukuda M, Kobata A). Oxford: Oxford University Press; 1993, pp. 165-185.
30. Packer N, Lawson M, Jardine D, Sanchez J, Gooley A: Analyzing glycoproteins separated by two-dimensional gel electrophoresis. Electrophoresis 1998, 19:981-988.
31. Charlwood J, Skehel J, Camilleri P: Analysis of N-linked oligosaccharides released from glycoproteins separated by two-dimensional gel electrophoresis. Anal Biochem 2000, 284:49-59.
32. Sagi D, Kienz P, Denecke J, Marquardt T, Peter-Katalinic J: Glycoproteomics of N-glycosylation by in-gel deglycosylation and matrix-assisted laser desorption/ionization-time of flight mass spectrometry mapping: application to congenital disorders of glycosylation. Proteomics 2005, 5:2689-2701.
33. Harvey D, Bateman R, Bordoli R, Tyldesley R: Ionization and fragmentation of complex glycans with a quadrupole time-of-flight mass spectrometer fitted with a matrix-assisted laser desorption/ ionization ion source. Rapid Commun Mass Spectrom 2000, 14:2135-2142.
34. Lewandrowski U, Resemann A, Sickmann A: Laser-induced dissociation/high-energy collisioninduced dissociation fragmentation using MALDI-TOF/TOF-MS instrumentation for the analysis of neutral and acidic oligosaccharides. Anal Chem 2005, 77:3274-3283.
35. Mechref Y, Novotny M, Krishnan C: Structural characterization of oligosaccharides using MALDI-TOF/TOF tandem mass spectrometry. Anal Chem 2003, 75:4895-4903.
36. Harvey D, Martin R, Jackson K, Sutton C: Fragmentation of N-linked glycans with a matrixassisted laser desorption/ionization ion trap time-of-flight mass spectrometer. Rapid Commun Mass Spectrom 2004, 18:2997-3007.
37. Zhang J, Schubothe K, Li B, Russell S, Lebrilla C: Infrared multiphoton dissociation of O-linked mucin-type oligosaccharides. Anal Chem 2005, 77:208-214.
38. Yamagaki T, Suzuki H, Tachibana K: In-source and postsource decay in negative-ion matrixassisted laser desorption/ionization time-of-flight mass spectrometry of neutral oligosaccharides. Anal Chem 2005, 77:1701-1707.
39. Robbe C, Capon C, Flahaut C, Michalski J: Microscale analysis of mucin-type O-glycans by a coordinated fluorophore-assisted carbohydrate electrophoresis and mass spectrometry approach. Electrophoresis 2003, 24:611-621.
40. Schulz B, Packer N, Karlsson N: Small-scale analysis of O-linked oligosaccharides from glycoproteins and mucins separated by gel electrophoresis. Anal Chem 2002, 74:6088-6097.
41. Zamfir A, Bindila L, Lion N, Allen M, Girault H, Peter-Katalinic J: Chip electrospray mass spectrometry for carbohydrate analysis. Electrophoresis 2005, 26:3650-3673.
42. An H, Peavy T, Hedrick JL, Lebrilla C: Determination of N-glycosylation sites and site heterogeneity in glycoproteins. Anal Chem 2003, 75:5628-5637.
43. Larsen M, Hojrup P, Roepstorff P: Characterization of gel-separated glycoproteins using twostep proteolytic digestion combined with sequential microcolumns and mass spectrometry. Mol Cell Proteomics 2005, 4:107-119.
44. Tajiri M, Yoshida S, Wada Y: Differential analysis of site-specific glycans on plasma and cellular fibronectins: application of a hydrophilic affinity method for glycopeptide enrichment. Glycobiology 2005, 15:1332-1340.
45. Håkansson K, Emmett M, Marshall A, Davidsson P, Nilsson C: Structural analysis of 2Dgel-separated glycoproteins from human cerebrospinal fluid by tandem high-resolution mass spectrometry. J Proteome Res 2003, 2:581-588.
46. Håkansson K, Cooper H, Hudgins R, Nilsson C: High resolution tandem mass spectrometry for structural biochemistry. Curr Org Chem 2003, 7:1503-1525.
47. Renfrow M, Cooper H, Tomana M, Kulhavy R, Hiki Y, Toma K, Emmett M, Mestecky J, Marshall A, Novak J: Determination of aberrant O-glycosylation in the IgA1 hinge region by electron capture dissociation Fourier transform-ion cyclotron resonance mass spectrometry. J Biol Chem 2005, 280:19136-19145.
48. Wada Y, Tajiri M, Yoshida S: Hydrophilic affinity isolation and MALDI multiple-stage tandem mass spectrometry of glycopeptides for glycoproteomics. Anal Chem 2004, 76:6560-6565.
49. Rademaker G, Pegantis S, Blok-Tip L, Langridge JI, Kleen A, Thomas-Oates JE: Mass spectrometric determination of the sites of O-glycan attachment with low picomolar sensitivity. Anal Biochem 1998, 257:149-160.
50. Wada Y, Azadi P, Costello C, Dell A, Dwek R, Geyer H, Geyer R, Kakehi K, Karlsson N, Kato K, et al.: Comparison of the methods for profiling glycoprotein glycans: HUPO HGPI (Human Proteome OrganizationHumanDisease Glycomics/Proteome Initiative) multi-institutional study. Glycobiology 2007, 17:411-422.
51. Cooper C, Gasteiger E, Packer N: GlycoMod-a software tool for determining glycosylation compositions from mass spectrometric data. Proteomics 2001, 1:340-349.
52. Cooper C, Joshi H, Harrison M, Wilkins M, Packer N: GlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources. Nucleic Acids Res 2003, 31:511-513.
53. Varki A,Marth J: Oligosaccharides in vertebrate development. Semin Dev Biol 1995, 6:127-138.
54. Lohmann K, von der Lieth C: GlycoFragment and GlycoSearchMS: web tools to support the interpretation of mass spectra of complex carbohydrates. Nucleic Acids Res 2004, 32:W261-W266.
55. Lütteke T, Bohne-Lang A, Loss A, Götz T, Frank M, von der Lieth C: GLYCOCIENCES.de: an Internet portal to support glycomics and glycobiology research. Glycobiology 2006, 16:71R-81R.
56. Lohmann K, von der Lieth C: GLYCO-FRAGMENT: A web tool to support the interpretation of mass spectra of complex carbohydrates. Proteomics 2003, 3:2028-2035.
57. Clerens S, Van den E, Verhaert P, Geenen L, Arckens L: Sweet Substitute: a software tool for in silico fragmentation of peptide-linked N-glycans. Proteomics 2004, 4:629-632.
58. Ethier M, Saba J, Spearman M, KrokhinO,ButlerM, Ens W, Standing K, Perreault H: Application of the StrOligo algorithm for the automated structure assignment of complex N-linked glycans from glycoproteins using tandem mass spectrometry. Rapid Commun Mass Spectrom 2003, 17:2713-2720.
59. Ethier M, Saba J, EnsW, Standing K, Perreault H: Automated structural assignment of derivatized complex N-linked oligosaccharides from tandem mass spectra. Rapid Commun Mass Spectrom 2002, 16:1743-1754.
60. Goldberg D, Sutton-Smith M, Paulson J, Dell A: Automatic annotation of matrix-assisted laser desorption/ionization N-glycan spectra. Proteomics 2005, 5:865-875.
61. van Halbeek H: 1H nuclear magnetic resonance spectroscopy of carbohydrate chains of glycoproteins. Methods Enzymol 1994, 230:132-168.
62. Edge C, Rademacher T, Wormald M, Parekh R, Butters T, Wing D, Dwek R: Fast sequencing of oligosaccharides: the reagent-array analysis method. Proc Natl Acad Sci USA 1992, 89:6338-6342.
63. Tseng K, Hedrick J, Lebrilla C: Catalog-library approach for the rapid and sensitive structural elucidation of oligosaccharides. Anal Chem 1999, 71:3747-3754.
64. Tang H, MechrefY,Novotny M: Automated interpretation ofMS/MS spectra of oligosaccharides. Bioinformatics 2005, 21:i431-i439.
65. AshlineD, Singh S, HannemanA,ReinholdV:Congruent strategies for carbohydrate sequencing. 1. Mining structural details by MS(n). Anal Chem 2005, 77:6250-6262.
66. Zhang H, Singh S, Reinhold V: Congruent strategies for carbohydrate sequencing. 2. FragLib: an MS(n) spectral library. Anal Chem 2005, 77:6263-6270.
67. Gaucher S, Morrow J, Leary J: STAT: a saccharide topology analysis tool used in combination with tandem mass spectrometry. Anal Chem 2000, 72:2331-2336.
68. Lapadula A, Hatcher P, Hanneman A, Ashline D, Zhang H, Reinhold V: Congruent strategies for carbohydrate sequencing. 3. OSCAR: an algorithm for assigning oligosaccharide topology from MS(n) data. Anal Chem 2005, 77:6271-6279.
69. Joshi H, Harrison M, Schulz B, Cooper C,Packer N, Karlsson N: Development of a mass fingerprinting tool for automated interpretation of oligosaccharide fragmentation data. Proteomics 2004, 4:1650-1664.
70. Kameyama A, Kikuchi N, Nakaya S, Ito H, Sato T, Shikanai T, Takahashi Y, Takahashi K, Narimatsu H: A strategy for identification of oligosaccharide structures using observational multistage mass spectral library. Anal Chem 2005, 77:4719-4725.