A method for N-terminal de novo sequence analysis of proteins by matrix-assisted laser desorption/ionization mass spectrometry

Analytical Biochemistry

Volumn 380, Issue 2, 2008, Pages 291-296

  Kuyama, Hiroki ^a   Sonomura, Kazuhiro ^b   Nishimura, Osamu ^a,b   Tsunasawa, Susumu ^a  

^a OSAKA UNIVERSITY   (Japan)

^b SHIMADZU CORPORATION   (Japan)

Author keywords

Mass spectrometry; N terminal modification; N terminal sequence analysis; Succinimidyloxycarbonylmethyl tris(2,4,6 trimethoxyphenyl)phosphonium bromide

Indexed keywords

CHEMICAL ANALYSIS; DESORPTION; PEPTIDES;

DE NOVO SEQUENCING; FRAGMENTATION PATTERNS; MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY; N-TERMINAL SEQUENCES; N-TERMINALS; SEQUENCE ANALYSIS; SUCCINIMIDYLOXYCARBONYLMETHYL TRIS(2,4,6-TRIMETHOXYPHENYL)PHOSPHONIUM BROMIDE; TANDEM MASS SPECTROMETRIC ANALYSIS;

MASS SPECTROMETRY;

ALPHA LACTALBUMIN; ANGIOTENSIN II; CARBONATE DEHYDRATASE II; CORTICOTROPIN[18-39]; HEMOGLOBIN; METALLOPROTEINASE; PEPTIDE; SUCCINIMIDE DERIVATIVE; SUCCINIMIDYLOXYCARBONYLMETHYLTRIS(2,4,6 TRIMETHOXYPHENYL)PHOSPHONIUM BROMIDE;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; CHEMICAL MODIFICATION; GRIFOLA; HUMAN; MASS SPECTROMETER; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; PEPTIDE ANALYSIS; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; TANDEM MASS SPECTROMETRY;

GRIFOLA FRONDOSA;

EID: 47749148064     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2008.05.053     Document Type: Article

References (27)

1. Chait B.T. Mass spectrometry: bottom-up or top-down?. Science 314 (2006) 65-66
2. Henzel W.J., Billeci T.M., Stults J.T., Wong S.C., Grimley C., and Watanabe C. Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Natl. Acad. Sci. USA 90 (1993) 5011-5015
3. Mann M., Hojrup P., and Roepstorff P. Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol. Mass Spectrom. 22 (1993) 338-345
4. James P., Quadroni M., Carafoli E., and Gonnet G. Protein identification by mass profile fingerprinting. Biochem. Biophys. Res. Commun. 195 (1993) 58-64
5. Yates J.R., Speicher S., Griffin P.R., and Hunkapiller T. Peptide mass maps: a highly informative approach to protein identification. Anal. Biochem. 214 (1993) 397-408
6. Eng J.K., McCormack A.L., and Yates J.R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5 (1994) 976-989
7. Mann M., and Wilm M. Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal. Chem. 66 (1994) 4390-4399
8. The FANTOM Consortium and RIKEN Genome Exploration Research Group and Genome Science Group, The transcriptional landscape of the mammalian genome, Science 309 (2005) 1559-1563.
9. Nakazawa T., Yamaguchi M., Okamura T., Ando E., Nishimura O., and Tsunasawa S. Terminal proteomics: N- and C-terminal analyses for high-fidelity identification of proteins using MS. Proteomics 8 (2008) 673-685
10. Wilkins M.R., Gasteiger E., Tonella L., Ou K., Tyler M., Sanchez J.C., Gooley A.A., Walsh B.J., Bairoch A., Appel R.D., Williams K.L., and Hochstrasser D.F. Protein identification with N and C-terminal sequence tags in proteome projects. J. Mol. Biol. 278 (1998) 599-608
11. Kuyama H., Shima K., Sonomura K., Yamaguchi M., Ando E., Nishimura O., and Tsunasawa S. A simple and highly successful C-terminal sequence analysis of proteins by mass spectrometry. Proteomics 8 (2008) 1539-1550
12. Huang Z.H., Wu J., Roth K.D.W., Yang Y., Gage D.A., and Watson J.T. A picomole-scale method for charge derivatization of peptides for sequence analysis by mass spectrometry. Anal. Chem. 69 (1997) 137-144
13. Huang Z.H., Shen T., Wu J., Gage D.A., and Watson J.T. Protein sequencing by matrix-assisted laser desorption ionization-postsource decay-mass spectrometry analysis of the N-tris(2,4,6-trimethoxyphenyl) phosphine-acetylated tryptic digests. Anal. Biochem. 268 (1999) 305-317
14. Nonaka T., Ishikawa H., Tsumuraya Y., Hashimoto Y., Dohmae N., and Takio K. Characterization of a thermostable lysine-specific metalloendopeptidase from the fruiting bodies of a basidiomycete, Grifola frondosa. J. Biochem. 118 (1995) 1014-1020
15. Nonaka T., Hashimoto Y., and Takio K. Kinetic characterization of lysine-specific metalloendopeptidases from Grifola frondosa and Pleurotus ostreatus fruiting bodies. J. Biochem. 124 (1998) 157-162
16. Hori T., Kumasaka T., Yamamoto M., Nonaka N., Tanaka N., Hashimoto Y., Ueki T., and Takio K. Structure of a new 'aspzincin' metalloendopeptidase from Grifola frondosa: implications for the catalytic mechanism and substrate specificity based on several different crystal forms. Acta Crystallogr. D 57 (2001) 361-368
17. Kuyama H., Sonomura K., and Nishimura O. Sensitive detection of phosphopeptides by matrix-assisted laser desorption/ionization mass spectrometry: use of alkylphosphonic acids as matrix additives. Rapid Commun. Mass Spectrom. 22 (2008) 1109-1116
18. Akiyama T.H., Sasagawa T., Suzuki M., and Titani K. A method for selective isolation of the amino-terminal peptide from α-amino-blocked proteins. Anal. Biochem. 222 (1994) 210-216
19. Gevaert K., Goethals M., Martens L., Van Damme J., Staes A., Thomas G.R., and Vandekerckhove J. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat. Biotechnol. 21 (2003) 566-569
20. Kuhn K., Thompson A., Prinz T., Muller J., Baumann C., Schmidt G., Neumann T., and Hamon C. Isolation of N-terminal protein sequence tags from cyanogen bromide cleaved proteins as a novel approach to investigate hydrophobic proteins. J. Proteome Res. 2 (2003) 598-609
21. McDonald L., Robertson D.H.L., Hurst J.L., and Beynon R.J. Positional proteomics: selective recovery and analysis of N-terminal proteolytic peptides. Nat. Methods 2 (2005) 955-957
22. Yamaguchi M., Nakazawa T., Kuyama H., Obama T., Ando E., Okamura T., Ueyama N., and Norioka S. High-throughput method for N-terminal sequencing of proteins by MALDI mass spectrometry. Anal. Chem. 77 (2005) 645-651
23. Zhou C., Zhang Y., Qin P., Liu X., Zhao L., Yang S., Cai Y., and Qian X. A method for rapidly confirming protein N-terminal sequences by matrix-assisted laser-desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 20 (2006) 2878-2884
24. Yamaguchi M., Obama T., Kuyama H., Nakayama D., Ando E., Okamura T., Ueyama N., Nakazawa T., Norioka S., Nishimura O., and Tsunasawa S. Specific isolation of N-terminal fragments from proteins and their high-fidelity de novo sequencing. Rapid Commun. Mass Spectrom. 21 (2007) 3329-3336
25. Mikami T., and Takao T. Selective isolation of N-blocked peptides by isocyanate-coupled resin. Anal. Chem. 79 (2007) 7910-7915
26. Coussot G., Hawke D.H., Mularz A., Koomen J.M., and Kobayashi R. A method for the isolation of blocked N-terminal peptides. Anal. Biochem. 361 (2007) 302-304
27. Wachter E., Machleidt W., Hofner H., and Otto J. Aminopropyl glass and its p -phenylene diisothiocyanate derivative, a new support in solid-phase Edman degradation of peptides and proteins. FEBS Lett. 35 (1973) 97-102