Computational framework for identification of intact glycopeptides in complex samples

Analytical Chemistry

Volumn 86, Issue 1, 2014, Pages 453-463

  Mayampurath, Anoop ^a   Yu, Chuan Yih ^a   Song, Ehwang ^b   Balan, Jagadheshwar ^a   Mechref, Yehia ^b   Tang, Haixu ^a  

^a INDIANA UNIVERSITY   (United States)

^b TEXAS TECH UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COLLISION-INDUCED DISSOCIATION; COMPUTATIONAL FRAMEWORK; ELECTRON-TRANSFER DISSOCIATION; HIGHER-ENERGY C-TRAP DISSOCIATIONS; HUMAN SERUM PROTEOME; MASS SPECTROMETRIC DATA; PROTEIN GLYCOSYLATION; PROTEIN MODIFICATIONS;

AMINO ACIDS; DISSOCIATION; ESTERIFICATION; GLYCOSYLATION; MASS SPECTROMETERS; MASS SPECTROMETRY; PLANTS (BOTANY); SUGARS;

PEPTIDES;

GLYCOPEPTIDE;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BIOLOGY; BLOOD; CATTLE; GENETICS; HUMAN; METHODOLOGY; MOLECULAR GENETICS; SWINE;

AMINO ACID SEQUENCE; ANIMALS; CATTLE; COMPUTATIONAL BIOLOGY; GLYCOPEPTIDES; HUMANS; MOLECULAR SEQUENCE DATA; SWINE;

EID: 84891784931     PISSN: 00032700     EISSN: 15206882     Source Type: Journal    
DOI: 10.1021/ac402338u     Document Type: Article

References (51)

1. Varki, A.; Cummings, R. D.; Esko, J. D.; Freeze, H. H.; Stanley, P.; Bertozzi, C. R.; Hart, G. W.; Etzler, M. E. Essentials of Glycobiology, 2 nd ed.; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY, 2008.
2. Dwek, R. A. Chem. Rev. 1996, 96, 683-720
3. Valliere-Douglass, J. F.; Eakin, C. M.; Wallace, A.; Ketchem, R. R.; Wang, W.; Treuheit, M. J.; Balland, A. J. Biol. Chem. 2010, 285, 16012-16022
4. Rademacher, T. W.; Parekh, R. B.; Dwek, R. A. Annu. Rev. Biochem. 1988, 57, 785-838
5. Kooyk, Y. v.; Rabinovich, G. A. Nat. Immunol. 2008, 9, 9
6. Mechref, Y.; Hu, Y.; Garcia, A.; Zhou, S.; Desantos-Garcia, J. L.; Hussein, A. Bioanalysis 2012, 4, 2457-2469
7. An, H. J.; Kronewitter, S. R.; Leoz, M. L. A. d.; Lebrilla, C. B. Curr. Opin. Chem. Biol. 2009, 13, 601-607
8. Lebrilla, C. B.; An, H. J. Mol. BioSyst. 2009, 5, 17-20
9. Mechref, Y.; Hu, Y.; Garcia, A.; Hussein, A. Electrophoresis 2012, 33, 1755-1767
10. An, H. J.; Miyamoto, S.; Lancaster, K. S.; Kirmiz, C.; Li, B.; Lam, K. S.; Leiserowitz, G. S.; Lebrilla, C. B. J. Proteome Res. 2006, 5, 1626-1635
11. Kirmiz, C.; Li, B.; An, H. J.; Clowers, B. H.; Chew, H. K.; Lam, K. S.; Ferrige, A.; Alecio, R.; Borowsky, A. D.; Sulaimon, S.; Lebrilla, C. B.; Miyamoto, S. Mol. Cell. Proteomics 2007, 6, 43-55
12. Arnold, J. N.; Saldova, R.; Hamid, U. M. A.; Rudd, P. M. Proteomics 2008, 8, 3284-3293
13. Mayampurath, A.; Yu, C.-Y.; Mechref, Y.; Tang, H. Curr. Proteomics 2011, 8, 309-324
14. Zaia, J. OMICS 2010, 14, 401-418
15. Wuhrer, M.; Catalina, I. M.; Deelder, A. M.; Hokke, C. H. J. Chromatogr., B 2006, 849, 115-128
16. Mechref, Y. In Current Protocols in Protein Science; John Wiley & Sons, Inc.: Brooklyn, NY, 2001.
17. Peter-Katalinic, J. Methods Enzymol. 2005, 405, 139-71
18. Medzihradszky, K. F. Methods Enzymol. 2005, 405, 116-138
19. Scott, N. E.; Parker, B. L.; Connolly, A. M.; Paulech, J.; Edwards, A. V. G.; Crossett, B.; Falconer, L.; Kolarich, D.; Djordjevic, S. P.; HÃ̧jrup, P.; Packer, N. H.; Larsen, M. R.; Cordwell, S. J. Mol. Cell. Proteomics 2011, 10 M000031-MCP201
20. Singh, C.; Zampronio, C. G.; Creese, A. J.; Cooper, H. J. J. Proteome Res. 2012, 11, 4517-4525
21. Snovida, S. I.; Bodnar, E. D.; Viner, R.; Saba, J.; Perreault, H. l. n. Carbohydr. Res. 2010, 345, 792-801
22. Domon, B.; Costello, C. E. Glycoconjugate 1988, 5
23. Ethier, M.; Saba, J. A.; Spearman, M.; Krokhin, O.; Butler, M.; Ens, W.; Standing, K. G.; Perreault, H. Rapid Commun. Mass Spectrom. 2003, 17, 2713-2720
24. Lapadula, A. J.; Hatcher, P. J.; Hanneman, A. J.; Ashline, D. J.; Zhang, H.; Reinhold, V. N. Anal. Chem. 2005, 77, 6271-6279
25. Goldberg, D.; Bern, M.; Parry, S.; Sutton-Smith, M.; Panico, M.; Morris, H. R.; Dell, A. J. Proteome Res. 2007, 6, 3995-4005
26. Hongsachart, P.; Huang-Liu, R.; Sinchaikul, S.; Pan, F.-M.; Phutrakul, S.; Chaung, Y.-M.; Chen, S.-T. Electrophoresis 2009, 30, 1206-1220
27. An, H. J.; Tillinghast, J. S.; Woodruff, D. L.; Rocke, D. M.; Lebrilla, C. B. J. Proteome Res. 2006, 5, 2800-2808
28. Wu, Y.; Mechref, Y.; Klouckova, I.; Mayampurath, A. M.; Novotny, M. V.; Tang, H. Rapid Commun. Mass Spectrom. 2009, 24, 965-72
29. Woodin, C. L.; Hua, D.; Maxon, M.; Rebecchi, K. R.; Go, E. P.; Desaire, H. Anal. Chem. 2012, 84, 4821-4829
30. Segu, Z.; Mechref, Y. Rapid Commun. Mass Spectrom. 2010, 24, 1217-1225
31. Mayampurath, A. M.; Wu, Y.; Segu, Z. M.; Mechref, Y.; Tang, H. Rapid Commun. Mass Spectrom. 2011, 25, 2007-2019
32. Catalina, I. M.; Koeleman, C. A. M.; Deelder, A. M.; Wuhrer, M. Rapid Commun. Mass Spectrom. 2007, 21, 1053-1061
33. Kandasamy, K.; Pandey, A.; Molina, H. Anal. Chem. 2009, 81, 7170-7180
34. Chalkley, R. J.; Medzihradszky, K. F.; Lynn, A. J.; Baker, P. R.; Burlingame, A. L. Anal. Chem. 2009, 82, 579-584
35. Baker, P. R.; Medzihradszky, K. F.; Chalkley, R. J. Mol. Cell. Proteomics 2010, 9, 1795-1803
36. Darula, Z.; Chalkley, R. J.; Baker, P.; Medzihradszky, K. F. Amino Acids 2011, 41, 321-8
37. Desaire, H. Presented at the 4th Charles Warren Workshop, Athens, GA, U.S.A., 2012.
38. Zhu, Z. Presented at the 60th ASMS Conference on Mass Spectrometry and Allied Topics, Vancouver, BC, 2012.
39. Zhu, Z.; Hua, D.; Clark, D. F.; Go, E. P.; Desaire, H. Anal. Chem. 2013, 85, 5023-5032
40. Perkins, D. N.; Pappin, D. J. C.; Creasy, D. M.; Cottrell, J. S. Electrophoresis 1999, 20, 3551-3567
41. Jain, E.; Bairoch, A.; Duvaud, S.; Phan, I.; Redaschi, N.; Suzek, B. E.; Martin, M. J.; McGarvey, P.; Gasteiger, E. BMC Bioinf. 2009, 10 136 10.1186/1471-2105-10-136
42. Consortium, T. U. Nucleic Acids Res. 2011, 39, 214-219
43. Renard, B. Y.; Kirchner, M.; Monigatti, F.; Ivanov, A. R.; Rappsilber, J.; Winter, D.; Steen, J. A. J.; Hamprecht, F. A.; Steen, H. Proteomics 2009, 9, 4978-4984
44. Elias, J. E.; Gygi, S. P. Nat. Meth 2007, 4, 207-214
45. Green, E. D.; Adelt, G.; Baenziger, J. U.; Wilson, S.; Van Halbeek, H. J. Biol. Chem. 1988, 263, 18253-68
46. Cooper, C. A.; Joshi, H. J.; Harrison, M. J.; Wilkins, M. R.; Packer, N. H. Nucleic Acids Res. 2003, 31, 511-513
47. Raman, R.; Venkatraman, M.; Ramakrishnan, S.; Lang, W.; Raguram, S.; Sasisekharan, R. Glycobiology 2006, 16, 82R-90R
48. Aldredge, D.; An, H. J.; Tang, N.; Waddell, K.; Lebrilla, C. B. J. Proteome Res. 2012, 11, 1958-1968
49. Liu, T.; Qian, W.-J.; Gritsenko, M. A.; Camp, D. G.; Monroe, M. E.; Moore, R. J.; Smith, R. D. J. Proteome Res. 2005, 4, 2070-2080
50. Zhang, H.; Li, X.-j.; Martin, D. B.; Aebersold, R. Nat. Biotechnol. 2003, 21, 660-666
51. Madera, M.; Mechref, Y.; Klouckova, I.; Novotny, M. V. J. Proteome Res. 2006, 5, 2348-2363