MAGIC: An automated N-linked glycoprotein identification tool using a y1-ion pattern matching algorithm and in silico MS2 approach

Analytical Chemistry

Volumn 87, Issue 4, 2015, Pages 2466-2473

  Lynn, Ke Shiuan ^a   Chen, Chen Chun ^b,d   Lih, T Mamie ^a,e   Cheng, Cheng Wei ^a   Su, Wan Chih ^c   Chang, Chun Hao ^a   Cheng, Chia Ying ^a   Hsu, Wen Lian ^a   Chen, Yu Ju ^c,d   Sung, Ting Yi ^a  

^a INSTITUTE OF INFORMATION SCIENCE   (Taiwan)

^b GENOMICS RESEARCH CENTER   (Taiwan)

^c INSTITUTE OF CHEMISTRY   (Taiwan)

^d NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^e NATIONAL YANG MING UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI; GLYCOPROTEINS; GLYCOSYLATION; ION ENGINES; IONS; LANTHANUM COMPOUNDS; MASS SPECTROMETRY; MIXTURES; PATTERN MATCHING; POLYSACCHARIDES; SEARCH ENGINES;

COLLISION-INDUCED DISSOCIATION SPECTRA; DATABASE SEARCHES; FALSE DISCOVERY RATE; HORSERADISH PEROXIDASE; IDENTIFICATION TOOLS; N-LINKED GLYCOPROTEINS; PATTERN MATCHING ALGORITHMS; RELATIVE INTENSITY;

PEPTIDES;

GLYCOPEPTIDE;

ALGORITHM; AUTOMATION; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; ESCHERICHIA COLI; FACTUAL DATABASE; HELA CELL LINE; HUMAN;

ALGORITHMS; AUTOMATION; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; ESCHERICHIA COLI; GLYCOPEPTIDES; HELA CELLS; HUMANS; SOFTWARE;

EID: 84923167627     PISSN: 00032700     EISSN: 15206882     Source Type: Journal    
DOI: 10.1021/ac5044829     Document Type: Article

References (64)

1. Helenius, A.; Aebi, M. Science 2001, 291, 2364-2369
2. Alley, W. R., Jr. Chem. Rev. 2013, 113, 2668-2732
3. Ruiz-May, E. Front. Plant Sci. 2012, 3, 117
4. Meany, D. L.; Chan, D. W. Clin. Proteomics 2011, 8, 7
5. Hwang, H. Mass Spectrom Rev. 2010, 29, 79-125
6. Freeze, H. H. Lancet Neurol. 2012, 11, 453-466
7. Hennet, T. Biochim. Biophys. Acta 2012, 1820, 1306-1317
8. Suzuki, E. Clin. Cancer Res. 2007, 13, 1875-1882
9. Drake, P. M. Clin. Chem. 2010, 56, 223-236
10. Durand, G.; Seta, N. Clin. Chem. 2000, 46, 795-805
11. Li, D. Clin. Chim. Acta 2001, 313, 15-19
12. Ludwig, J. A.; Weinstein, J. N. Nat. Rev. Cancer 2005, 5, 845-856
13. Lazar, I. M. Electrophoresis 2011, 32, 3-13
14. Medzihradszky, K. F. Methods Enzymol. 2005, 405, 116-138
15. Novotny, M. V.; Mechref, Y. J. Sep. Sci. 2005, 28, 1956-1968
16. Domon, B.; Costello, C. E. Glycoconjugate J. 1988, 5, 397-409
17. Li, F. Proteomics 2013, 13, 341-354
18. Cooper, C. A. Proteomics 2001, 1, 340-349
19. Go, E. P. Anal. Chem. 2007, 79, 1708-1713
20. Ren, J. M. J. Proteome Res. 2007, 6, 3162-3173
21. Deshpande, N. J. Proteome Res. 2010, 9, 1063-1075
22. Irungu, J. Anal. Chem. 2007, 79, 3065-3074
23. Woodin, C. L. Anal. Chem. 2012, 84, 4821-4829
24. Pompach, P. J. Proteome Res. 2012, 11, 1728-1740
25. Goldberg, D. J. Proteome Res. 2007, 6, 3995-4005
26. Bern, M.; Current Protocols in Bioinformatics; Wiley: New York, 2012, Chapter 13, Unit 13.20.
27. He, L. J. Proteome Res. 2014, 13, 3881-3895
28. Ozohanics, O. Rapid Commun. Mass Spectrom. 2008, 22, 3245-3254
29. Wu, Y. Rapid Commun. Mass Spectrom. 2010, 24, 965-972
30. Nwosu, C. C. J. Proteome Res. 2011, 10, 2612-2624
31. Strum, J. S. Anal. Chem. 2013, 85, 5666-5675
32. Wu, S. W. J. Proteomics 2013, 84, 1-16
33. Dallas, D. C. Briefings Bioinf. 2013, 14, 361-374
34. Woodin, C. L. Analyst 2013, 138, 2793-2803
35. Segu, Z. M.; Mechref, Y. Rapid Commun. Mass Spectrom. 2010, 24, 1217-1225
36. Trinidad, J. C. Mol. Cell Proteomics 2013, 12, 3474-3488
37. Han, C. L. Mol. Cell Proteomics 2008, 7, 1983-1997
38. Zhao, P. J. Proteome Res. 2011, 10, 4088-4104
39. Balog, C. I. A. Mol. Cell. Proteomics 2010, 9, 667-681
40. Lin, C. W. Glycobiology 2011, 21, 530-542
41. Fiedler, K.; Simons, K. Cell 1995, 81, 309-312
42. Yang, B. Y. Carbohydr. Res. 1996, 287, 203-212
43. Zhou, W. Chem. Commun. (Cambridge) 2008, 5577-5579
44. Ma, Z. Q. J. Proteome Res. 2011, 10, 2896-2904
45. Schluesener, D. Proteomics 2005, 5, 1317-1330
46. Thaysen-Andersen, M. Anal. Chem. 2009, 81, 3933-3943
47. Satomi, Y. Rapid Commun. Mass Spectrom. 2004, 18, 2983-2988
48. Apweiler, R. Nucleic Acids Res. 2014, 42, D191-D198
49. Malerod, H. J. Proteome Res. 2013, 12, 248-259
50. Ashburner, M. Nat. Genet. 2000, 25, 25-29
51. CFG Functional Glycomics Gateway. http://www.functionalglycomics.org/glycomics/molecule/jsp/carbohydrate/carbMoleculeHome.jsp (accessed Dec. 1, 2014).
52. Campbell, M. P. Nucleic Acids Res. 2014, 42, D215-221
53. English, N. M. Cancer Res. 1998, 58, 3736-3742
54. Naor, D. Crit. Rev. Clin. Lab. Sci. 2002, 39, 527-579
55. Bartolazzi, A. J. Cell Biol. 1996, 132, 1199-1208
56. Lesley, J. J. Exp. Med. 1995, 182, 431-437
57. Han, H. Anal. Bioanal. Chem. 2012, 404, 373-388
58. Ponka, P.; Lok, C. N. Int. J. Biochem. Cell Biol. 1999, 31, 1111-1137
59. Hayes, G. R. Glycobiology 1995, 5, 227-232
60. Apweiler, R. Biochim. Biophys. Acta 1999, 1473, 4-8
61. Alves, P. Bioinformatics 2008, 24, 102-109
62. Hagglund, P. J. Proteome Res. 2004, 3, 556-566
63. Strader, M. B. Anal. Chem. 2006, 78, 125-134
64. Tsur, D. Nat. Biotechnol. 2005, 23, 1562-1567