Complexities and algorithms for glycan structure sequencing using tandem mass spectrometry

Series on Advances in Bioinformatics and Computational Biology

Volumn 5, Issue , 2007, Pages 297-306

  Shan, Baozhen ^a   Ma, Bin ^a   Zhang, Kaizhong ^a   Lajoie, Gilles ^a  

^a UNIVERSITY OF WESTERN ONTARIO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; HEURISTIC ALGORITHMS; HEURISTIC PROGRAMMING; MASS SPECTROMETRY; MOLECULAR BIOLOGY; PEPTIDES;

CELL MATRIX; DE NOVO SEQUENCING; GLYCAN DATABASE; GLYCAN STRUCTURES; GLYCOPEPTIDES; PRIMARY STRUCTURES; SOFTWARE PROGRAM; TANDEM MASS SPECTROMETRY;

POLYSACCHARIDES;

EID: 84857005983     PISSN: 17516404     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1142/9781860947995_0032     Document Type: Conference Paper

References (19)

1. K. Aebersold and M. Mann. Mass spectrometry-based protemics. Nature, 422:198-207, 2003.
2. V. Bafna and N. Edwards. On de novo interpretation of tandem mass spectra for peptide identification. RECOMB 2003, 9-18, Berlin, Germany, 2003.
3. Chen, T., Kao, M-Y., Tepel, M., Rush J., and Church, G. 2001. A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry. J. Comp. Biology 8(3), 325-337.
4. C.A. Cooper, E. Gasteiger, and N.H. Packer. GlycoMod - A software tool for determining glycosylation compositions from mass spectrometric data. Proteomics, 1:340-349, 2000.
5. C.A. Cooper, H. Joshi, M. Harrison, M. Wilkins, and N Packer: GlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources. Nucleic Acids Res., 31:511-513, 2003.
6. A. Dell and H. R. Morris. Glycoprotein Structure Determination by Mass Spectrometry. Science, 291:2351-2356, 2001.
7. B. Domon and CE. Costello. A systematic nomenclature for carbohydrate fragmentations in FAB-MS/MS spectra of glycoconjugates. Glycoconjugate J., 5:397-409, 1988.
8. M. Ethier, et al.. Application of the StrOligo algorithm for the automated structure assignment of complex N-linked glycans from tandem mass spectrometry.Rapid Commun. Mass Spectrom., 17:2713-2720, 2003.
9. S.P. Gaucher, J. Morrow and J.A. Leary. A saccharide topology analysis tool used in combination with tandem mass spectrometry Anal. Chem., 72:2231-2236, 2000.
10. D. Goldberg, M. Sutton-Smith, J. Paulson and Anne Dell. Automatic annotation of matrixassisted laser desorption/ionization N-glycan spectra. Proteomics, 5:865-875, 2005.
11. Michael R. Garey and David S. Johnson. Computers and intractability: a guide to the theory of NP-completeness. pp221, W.H. Freeman and Company, San Franciso 1979.
12. K. Keykhosravani, A. Doherty-Kirby, C. Zhang, A. Goldberg, G.K. Hunter and G. Lajoie. Comprehensive identification of posttranslational modifications in rat bone osteopontin by mass spectrometry. Biochemistry, 44:6990-7003, 2005.
13. B. Ma et. al. PEAKS: Powerful Software for Peptide De Novo Sequencing by Tandem Mass Spectrometry. Rapid Comm. in Mass Spectrom. 17(20):2337-2342. 2003.
14. Y. Mizuno and T. Sasagawa. An automated interpretation of MALDI/TOF postsource decay spectra of oligosaccharides. 1. Automated Peak Assignment. Anal. Chem., 71:4764-4771, 1999.
15. B. Shan, K. Zhang, B. Ma, C. Zhang and G. Lajorie. An Algorithm for Determining Glycan Structures from MS/MS Spectra. Proceedings of ICBA 2004, Florida, USA, 2004, in Advanced in bioinformatics and its applications, 414-425, World Scicntific, 2004.
16. H. Tang, Y. Mechref, and M.V. Novotny. Automated interpretation of MS/MS spectra of oligosaccharides. Bioinformatics 21:i431-i439, 2005.
17. M.E. Taylor and K. Drickamer. Introduction to Glycobiology. Oxford University Press, 2003.
18. J. Zala. Mass Spectrometry of Oligosaccharides. Mass Spectrometry Reviews, 23161-227, 2004.
19. C. Zhang, A. Doherty-Kirby and G. Lajoie. Investigation of Cationic Peanut Peroxidase Glycans by Electrospray Ionization Mass Spectrometry. Phytochemistry, 65:1575-88, 2004.