New glycoproteomics software, glycopep evaluator, generates decoy glycopeptides de novo and enables accurate false discovery rate analysis for small data sets

Analytical Chemistry

Volumn 86, Issue 18, 2014, Pages 9212-9219

  Zhu, Zhikai ^a   Su, Xiaomeng ^a   Go, Eden P ^a   Desaire, Heather ^a  

^a UNIVERSITY OF KANSAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DATABASE SYSTEMS; DISSOCIATION; ESTERIFICATION; GLYCOSYLATION; MASS SPECTROMETRY; MOLECULAR BIOLOGY; SEARCH ENGINES;

CELLULAR ACTIVITIES; COLLISION-INDUCED DISSOCIATION; CONSENSUS SEQUENCE; DATABASE SEARCHES; ELECTRON-TRANSFER DISSOCIATION; FALSE DISCOVERY RATE; PROTEIN GLYCOSYLATION; TANDEM MASS SPECTROMETRY;

PEPTIDES;

GLYCOPEPTIDE; PEPTIDE HYDROLASE; PLASMA PROTEIN;

AMINO ACID SEQUENCE; COMPUTER INTERFACE; COMPUTER PROGRAM; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; INTERNET; ISOLATION AND PURIFICATION; LABORATORY DIAGNOSIS; METABOLISM; MOLECULAR GENETICS; PROTEIN DATABASE; PROTEOMICS; TANDEM MASS SPECTROMETRY;

AMINO ACID SEQUENCE; BLOOD PROTEINS; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; DATABASES, PROTEIN; FALSE POSITIVE REACTIONS; GLYCOPEPTIDES; HUMANS; INTERNET; MOLECULAR SEQUENCE DATA; PEPTIDE HYDROLASES; PROTEOMICS; SOFTWARE; TANDEM MASS SPECTROMETRY; USER-COMPUTER INTERFACE;

EID: 84912096318     PISSN: 00032700     EISSN: 15206882     Source Type: Journal    
DOI: 10.1021/ac502176n     Document Type: Article

References (42)

1. Apweiler, R.; Hermjakob, H.; Sharon, N. Biochim. Biophys. Acta- Gen. Subj. 1999, 1473, 4-8.
2. Khoury, G. A.; Baliban, R. C.; Floudas, C. A. Sci. Rep. 2011, 1.
3. Banerjee, S.; Vishwanath, P.; Cui, J.; Kelleher, D. J.; Gilmore, R.; Robbins, P. W.; Samuelson, J. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 11676-11681.
4. Banks, D. D. J. Mol. Biol. 2011, 412, 536-550.
5. Furukawa, K.; Ohkawa, Y.; Yamauchi, Y.; Hamamura, K.; Ohmi, Y. J. Biochem. 2012, 151, 573-578.
6. Van den Steen, P.; Rudd, P. M.; Dwek, R. A.; Opdenakker, G. Crit. Rev. Biochem. Mol. Biol. 1998, 33, 151-208.
7. Coelho, V.; Krysov, S.; Ghaemmaghami, A. M.; Emara, M.; Potter, K. N.; Johnson, P.; Packham, G.; Martinez-Pomares, L.; Stevenson, F. K. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 18587-18592.
8. Wang, Y.; Tan, J.; Sutton-Smith, M.; Ditto, D.; Panico, M.; Campbell, R. M.; Varki, N. M.; Long, J. M.; Jaeken, J.; Levinson, S. R.; Wynshaw-Boris, A.; Morris, H. R.; Le, D.; Dell, A.; Schachter, H.; Marth, J. D. Glycobiology 2001, 11, 1051-1070.
9. Li, Y.; Tian, Y. A.; Rezai, T.; Prakash, A.; Lopez, M. F.; Chan, D. W.; Zhang, H. Anal. Chem. 2011, 83, 240-245.
10. Leymarie, N.; Zaia, J. Anal. Chem. 2012, 84, 3040-3048.
11. Desaire, H. Mol. Cell. Proteomics 2013, 12, 893-901.
12. Hong, Q.; Lebrilla, C. B.; Miyamoto, S.; Ruhaak, L. R. Anal. Chem. 2013, 85, 8585-93.
13. Desaire, H.; Hua, D. Int. J. Mass Spectrom. 2009, 287, 21-26.
14. Woodin, C. L.; Maxon, M.; Desaire, H. Analyst 2013, 138, 2793-2803.
15. Ceroni, A.; Maass, K.; Geyer, H.; Geyer, R.; Dell, A.; Haslam, S. M. J. Proteome Res. 2008, 7, 1650-1659.
16. Premier Biosoft. http://www.premierbiosoft.com/glycan/index. html (accessed April 30, 2014).
17. Goldberg, D.; Bern, M.; Parry, S.; Sutton-Smith, M.; Panico, M.; Morris, H. R.; Dell, A. J. Proteomics Res. 2007, 6, 3995-4005.
18. Apte, A.; Meitei, N. S. Methods Mol. Biol. 2010, 600, 269-81.
19. Chandler, K. B.; Pompach, P.; Goldman, R.; Edwards, N. J. Proteome Res. 2013, 12, 3652-3666.
20. Bruker Daltonics. http://glycomics.ccrc.uga.edu/ GlycomicsPortal/showEntry.action?id=116 (accessed April 30, 2014).
21. Strum, J. S.; Nwosu, C. C.; Hua, S.; Kronewitter, S. R.; Seipert, R. R.; Bachelor, R. J.; An, H. J.; Lebrilla, C. B. Anal. Chem. 2013, 85, 5666-5675.
22. Mayampurath, A.; Yu, C. Y.; Song, E. W.; Balan, J.; Mechref, Y.; Tang, H. X. Anal. Chem. 2014, 86, 453-463.
23. Woodin, C. L.; Hua, D.; Maxon, M.; Rebecchi, K. R.; Go, E. P.; Desaire, H. Anal. Chem. 2012, 84, 4821-4829.
24. Zhu, Z.; Hua, D.; Clark, D. F.; Go, E. P.; Desaire, H. Anal. Chem. 2013, 85, 5023-5032.
25. Nesvizhskii, A. I.; Vitek, O.; Aebersold, R. Nat. Methods 2007, 4, 787-797.
26. Elias, J. E.; Gygi, S. P. Nat. Methods 2007, 4, 207-214.
27. Choi, H.; Nesvizhskii, A. I. J. Proteome Res. 2008, 7, 47-50.
28. Kall, L.; Storey, J. D.; MacCoss, M. J.; Noble, W. S. J. Proteome Res. 2008, 7, 29-34.
29. Nesvizhskii, A. I. J. Proteomics 2010, 73, 2092-2123.
30. Huttlin, E. L.; Hegeman, A. D.; Harms, A. C.; Sussman, M. R. J. Proteome Res. 2006, 6, 392-398.
31. Reiter, L.; Claassen, M.; Schrimpf, S. P.; Jovanovic, M.; Schmidt, A.; Buhmann, J. M.; Hengartner, M. O.; Aebersold, R. Mol. Cell. Proteomics 2009, 8, 2405-2417.
32. Reidegeld, K. A.; Eisenacher, M.; Kohl, M.; Chamrad, D.; Korting, G.; Blueggel, M.; Meyer, H. E.; Stephan, C. Proteomics 2008, 8, 1129-1137.
33. Wang, G.; Wu, W. W.; Zhang, Z.; Masilamani, S.; Shen, R. F. Anal. Chem. 2009, 81, 146-159.
34. Gupta, N.; Bandeira, N.; Keich, U.; Pevzner, P. A. J. Am. Soc. Mass Spectrom. 2011, 22, 1111-1120.
35. Chalkley, R. J. J. Proteome Res. 2013, 12, 1062-1064.
36. Go, E. P.; Chang, Q.; Liao, H. X.; Sutherland, L. L.; Alam, S. M.; Haynes, B. F.; Desaire, H. J. Proteome Res. 2009, 8, 4231-4242.
37. Zhu, Z.; Su, X.; Clark, D. F.; Go, E. P.; Desaire, H. Anal. Chem. 2013, 85, 8403-8411.
38. Zhu, Z.; Go, E. P.; Desaire, H. J. Am. Soc. Mass Spectrom. 2014, 25, 1012-1017.
39. Alley, W. R.; Mechref, Y.; Novotny, M. V. Rapid Commun. Mass Spectrom. 2009, 23, 161-170.
40. Wada, Y.; Azadi, P.; Costello, C. E.; Dell, A.; Dwek, R. A.; Geyer, H.; Geyer, R.; Kakehi, K.; Karlsson, N. G.; Kato, K.; Kawasaki, N.; Khoo, K. H.; Kim, S.; Kondo, A.; Lattova, E.; Mechref, Y.; Miyoshi, E.; Nakamura, K.; Narimatsu, H.; Novotny, M. V.; Packer, N. H.; Perreault, H.; Peter-Katalinic, J.; Pohlentz, G.; Reinhold, V. N.; Rudd, P. M.; Suzuki, A.; Taniguchi, N. Glycobiology 2007, 17, 411-422.
41. Zhang, Y.; Go, E. P.; Desaire, H. Anal. Chem. 2008, 80, 3144-3158.
42. Cooper, C. A.; Gasteiger, E.; Packer, N. H. Proteomics 2001, 1, 340-349.