C-terminal de novo sequencing of peptides using oxazolone-based derivatization with bromine signature

Analytical Biochemistry

Volumn 419, Issue 2, 2011, Pages 211-216

  Kim, Jong Seo ^a   Shin, Mansup ^a   Song, Jin Su ^a   An, Songhie ^a   Kim, Hie Joon ^a  

^a Seoul National University   (South Korea)

Author keywords

Br signature; C terminal; De novo sequencing; Derivatization; Oxazolone

Indexed keywords

BROMINE;

BROMINE SIGNATURES; CARBOXYLIC GROUP; DE NOVO SEQUENCING; DERIVATIZATIONS; MS/MS ANALYSIS; OXAZOLONE; TERMINAL MODIFICATIONS; TERMINAL SEQUENCING;

PEPTIDES;

BROMINE; CARBOXYLIC ACID; ION; OXAZOLONE; PEPTIDE;

ARTICLE; BIOCHEMISTRY; CARBOXY TERMINAL SEQUENCE; PRIORITY JOURNAL; PROTEIN MODIFICATION; SEQUENCE ANALYSIS; TANDEM MASS SPECTROMETRY;

EID: 80054063140     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2011.08.011     Document Type: Article

References (41)

1. M. Yamaguchi, T. Nakazawa, H. Kuyama, T. Obama, E. Ando, T.A. Okamura, N. Ueyama, and S. Norioka High-throughput method for N-terminal sequencing of proteins by MALDI mass spectrometry Anal. Chem. 77 2005 645 651
2. M. Yamaguchi, T. Obama, H. Kuyama, D. Nakayama, E. Ando, T.A. Okamura, N. Ueyama, T. Nakazawa, S. Norioka, O. Nishimura, and S. Tsunasawa Specific isolation of N-terminal fragments from proteins and their high-fidelity de novo sequencing Rapid Commun. Mass Spectrom. 21 2007 3329 3336
3. M. Yamaguchi, D. Nakayama, K. Shima, H. Kuyama, E. Ando, T.A. Okamura, N. Ueyama, T. Nakazawa, S. Norioka, O. Nishimura, and S. Tsunasawa Selective isolation of N-terminal peptides from proteins and their de novo sequencing by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry without regard to unblocking or blocking of N-terminal amino acids Rapid Commun. Mass Spectrom. 22 2008 3313 3319
4. Y.H. Lee, M.S. Kim, W.S. Choie, H.K. Min, and S.W. Lee Highly informative proteome analysis by combining improved N-terminal sulfonation for de novo peptide sequencing and online capillary reverse-phase liquid chromatography/tandem mass spectrometry Proteomics 4 2004 1684 1694
5. R.L. Beardsley, L.A. Sharon, and J.P. Reilly Peptide de novo sequencing facilitated by a dual-labeling strategy Anal. Chem. 77 2005 6300 6309
6. J.S. Kim, E. Cui, and H.J. Kim Picolinamidination of phosphopeptides for MALDI-TOF-TOF mass spectrometric sequencing with enhanced sensitivity J. Am. Soc. Mass Spectrom. 20 2009 1751 1758
7. M. Lee, M. Kang, B. Moon, and H.B. Oh Gas-phase peptide sequencing by TEMPO-mediated radical generation Analyst 134 2009 1706 1712
8. Y.H. Lee, H. Han, S.B. Chang, and S.W. Lee Isotope-coded N-terminal sulfonation of peptides allows quantitative proteomic analysis with increased de novo peptide sequencing capability Rapid Commun. Mass Spectrom. 18 2004 3019 3027
9. E. Guillaume, A. Panchaud, M. Affolter, V. Desvergnes, and M. Kussmann Differentially isotope-coded N-terminal protein sulphonation: combining protein identification and quantification Proteomics 6 2006 2338 2349
10. M.J. Noga, A. Asperger, and J. Silberring N-Terminal H-3/D-3-acetylation for improved high-throughput peptide sequencing by matrix-assisted laser desorption/ionization mass spectrometry with a time-of-flight/time-of-flight analyzer Rapid Commun. Mass Spectrom. 20 2006 1823 1827
11. F. Wang, H. Fu, Y. Jiang, and Y. Zhao A picomole-scale method for rapid peptide sequencing through convenient and efficient N-terminal phosphorylation and electrospray ionization mass spectrometry J. Am. Soc. Mass Spectrom. 17 2006 995 999
12. M.L. Hennrich, S. Mohammed, A.F. Altelaar, and A.J. Heck Dimethyl isotope labeling assisted de novo peptide sequencing J. Am. Soc. Mass Spectrom. 21 2010 1957 1965
13. J.C. Timmer, M. Enoksson, E. Wildfang, W. Zhu, Y. Igarashi, J.B. Denault, Y. Ma, B. Dummitt, Y.H. Chang, A.E. Mast, A. Eroshkin, J.W. Smith, W.A. Tao, and G.S. Salvesen Profiling constitutive proteolytic events in vivo Biochem. J. 407 2007 41 48
14. S. Mahrus, J.C. Trinidad, D.T. Barkan, A. Sali, A.L. Burlingame, and J.A. Wells Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini Cell 134 2008 866 876
15. G. Xu, S.B. Shin, and S.R. Jaffrey Global profiling of protease cleavage sites by chemoselective labeling of protein N-termini Proc. Natl. Acad. Sci. USA 106 2009 19310 19315
16. O. Kleifeld, A. Doucet, U. auf dem Keller, A. Prudova, O. Schilling, R.K. Kainthan, A.E. Starr, L.J. Foster, J.N. Kizhakkedathu, and C.M. Overall Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products Nat. Biotechnol. 28 2010 281 288
17. B. Samyn, K. Sergeant, P. Castanheira, C. Faro, and J. Van Beeumen A new method for C-terminal sequence analysis in the proteomic era Nat. Methods 2 2005 193 200
18. B. Samyn, K. Sergeant, and J. Van Beeumen A method for C-terminal sequence analysis in the proteomic era (proteins cleaved with cyanogen bromide) Nat. Protoc. 1 2006 318 323
19. W.E. Running, S. Ravipaty, J.A. Karty, and J.P. Reilly A top-down/bottom-up study of the ribosomal proteins of Caulobacter crescentus J. Proteome Res. 6 2007 337 347
20. S. Sechi, and B.T. Chait A method to define the carboxyl terminal of proteins Anal. Chem. 72 2000 3374 3378
21. H. Kuyama, K. Shima, K. Sonomura, M. Yamaguchi, E. Ando, O. Nishimura, and S. Tsunasawa A simple and highly successful C-terminal sequence analysis of proteins by mass spectrometry Proteomics 8 2008 1539 1550
22. H. Kuyama, C. Nakajima, T. Nakazawa, O. Nishimura, and S. Tsunasawa A new approach for detecting C-terminal amidation of proteins and peptides by mass spectrometry in conjunction with chemical derivatization Proteomics 9 2009 4063 4070
23. K. Sonomura, H. Kuyama, E. Matsuo, S. Tsunasawa, and O. Nishimura The specific isolation of C-terminal peptides of proteins through a transamination reaction and its advantage for introducing functional groups into the peptide Rapid Commun. Mass Spectrom. 23 2009 611 618
24. O. Schilling, O. Barre, P.F. Huesgen, and C.M. Overall Proteome-wide analysis of protein carboxy termini: C terminomics Nat. Methods 7 2010 508 511
25. D.R. Goodlett, A. Keller, J.D. Watts, R. Newitt, E.C. Yi, S. Purvine, J.K. Eng, P. Von Haller, R. Aebersold, and E. Kolker Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation Rapid Commun. Mass Spectrom. 15 2001 1214 1221
26. S. Julka, D. Dielman, and S.A. Young Detection of C-terminal peptide of proteins using isotope coding strategies J. Chromatogr. B 874 2008 101 110
27. P.P. Moerman, K. Sergeant, G. Debyser, B. Devreese, and B. Samyn A new chemical approach to differentiate carboxy terminal peptide fragments in cyanogen bromide digests of proteins J. Proteomics 73 2010 1454 1460
28. T. Nakazawa, M. Yamaguchi, K. Nishida, H. Kuyama, T. Obama, E. Ando, T.A. Okamura, N. Ueyama, K. Tanaka, and S. Norioka Enhanced responses in matrix-assisted laser desorption/ionization mass spectrometry of peptides derivatized with arginine via a C-terminal oxazolone Rapid Commun. Mass Spectrom. 18 2004 799 807
29. M. Yamaguchi, M. Oka, K. Nishida, M. Ishida, A. Hamazaki, H. Kuyama, E. Ando, T.A. Okamura, N. Ueyama, S. Norioka, O. Nishimura, S. Tsunasawa, and T. Nakazawa Enhancement of MALDI-MS spectra of C-terminal peptides by the modification of proteins via an active ester generated in situ from an oxazolone Anal. Chem. 78 2006 7861 7869
30. C. Nakajima, H. Kuyama, T. Nakazawa, O. Nishimura, and S. Tsunasawa A method for N-terminal de novo sequencing of N-alpha-blocked proteins by mass spectrometry Analyst 136 2011 113 119
31. 18O into peptide fragments and its application for protein sequencing by electrospray and matrix-assisted laser desorption/ionization mass spectrometry Electrophoresis 17 1996 945 953
32. W. Mo, T. Takao, and Y. Shimonishi Accurate peptide sequencing by post-source decay matrix-assisted laser desorption/ionization time-of-flight mass spectrometry Rapid Commun. Mass Spectrom. 11 1997 1829 1834
33. S. Gu, S. Pan, E.M. Bradbury, and X. Chen Use of deuterium-labeled lysine for efficient protein identification and peptide de novo sequencing Anal. Chem. 74 2002 5774 5785
34. F.L. Brancia, H. Montgomery, K. Tanaka, and S. Kumashiro Guanidino labeling derivatization strategy for global characterization of peptide mixtures by liquid chromatography matrix-assisted laser desorption/ionization mass spectrometry Anal. Chem. 76 2004 2748 2755
35. K. Miyazaki, and A. Tsugita C-terminal sequencing method for peptides and proteins by the reaction with a vapor of perfluoric acid in acetic anhydride Proteomics 4 2004 11 19
36. K. Miyazaki, and A. Tsugita C-terminal sequencing method for proteins in polyacrylamide gel by the reaction of acetic anhydride Proteomics 6 2006 2026 2033
37. M. Miyagi, M. Nakao, T. Nakazawa, I. Kato, and S. Tsunasawa A novel derivatization method with 5-bromonicotinic acid N-hydroxysuccinimide for determination of the amino acid sequences of peptides Rapid Commun. Mass Spectrom. 12 1998 603 608
38. J.S. Kim, J. Kim, J.M. Oh, and H.J. Kim Tandem mass spectrometric method for definitive localization of phosphorylation sites using bromine signature Anal. Biochem. 414 2011 294 296
39. J.S. Kim, S.U. Song, H.J. Kim, Simultaneous identification of tyrosine phosphorylation and sulfation sites utilizing tyrosine-specific bromination, J. Am. Soc. Mass Spectrom., 22 (2011) doi: 10.1007/s13361-011-0214-9.
40. J.S. Kim, J.Y. Kim, and H.J. Kim Suppression of matrix clusters and enhancement of peptide signals in MALDI-TOF mass spectrometry using nitrilotriacetic acid Anal. Chem. 77 2005 7483 7488
41. M. Shin, and H.J. Kim Peptide C-terminal sequence analysis by MALDI-TOF MS utilizing EDC coupling with Br signature Bull. Korean Chem. Soc. 32 2011 1183 1186