C-terminal ladder sequencing of peptides using an alternative nucleophile in carboxypeptidase Y digests

Analytical Biochemistry

Volumn 357, Issue 2, 2006, Pages 167-172

  Hamberg, Anders ^a   Kempka, Martin ^b   Sjödahl, Johan ^b   Roeraade, Johan ^b   Hult, Karl ^a  

^a ALBANOVA UNIVERSITY CENTER   (Sweden)

^b ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

Author keywords

2 Pyridylmethylamine; MALDI; Matrix assisted laser desorption ionization mass spectrometry; Transpeptidation

Indexed keywords

AMINO ACIDS; DESORPTION; LADDERS; MASS SPECTROMETRY; NUCLEOPHILES;

2-PYRIDYLMETHYLAMINE; AMINO ACID SEQUENCE; CATALYZED REACTIONS; MALDI; MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY; SEQUENCE COVERAGES; TERMINAL SEQUENCING; TRANSPEPTIDATION;

PEPTIDES;

2 PYRIDYLMETHYLAMINE; AMINO ACID; BOMBESIN; BUFFER; CARBOXYPEPTIDASE; CARBOXYPEPTIDASE C; CORTICOTROPIN RELEASING FACTOR RECEPTOR[6-33]; CORTICOTROPIN[7-38]; DIGESTANT; GLUCAGON; INSULIN; N ACETYL RENIN TETRADECAPEPTIDE; PEPTIDE; PEPTIDE FRAGMENT; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CATALYSIS; DIGESTION; GROUP STRUCTURE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; METHODOLOGY; PRIORITY JOURNAL; PROTEIN DEGRADATION; SEQUENCE ANALYSIS;

EID: 33748784378     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2006.07.025     Document Type: Article

References (25)

1. Lambert J.-P., Ethier M., Smith J.C., and Figeys D. Proteomics: From gel based to gel free. Anal. Chem. 77 (2005) 3771-3788
2. Patterson S.D., and Aebersold R.H. Proteomics: The first decade and beyond. Nat. Genet. 33 (2003) 311-323
3. Steen H., and Mann M. The ABC's (and XYZ's) of peptide sequencing. Nat. Rev. Mol. Cell Biol. 5 (2004) 711-799
4. Kuruma H., Egawa S., Oh-Ishi M., Kodera Y., and Maeda T. Proteome analysis of prostate cancer. Prostate Cancer Prostatic Dis. 8 (2005) 14-21
5. Komatsu S., Konishi H., Shen S., and Yang G. Rice proteomics. Mol. Cell. Proteom. 2 (2003) 2-10
6. Saxinger C., Conrads T.P., Goldstein D.J., and Veenstra T.D. Fully automated synthesis of (phospho)peptide array in microtiter plate wells provides efficient access to protein tyrosine kinase characterisation. BMC Immunol. 6 (2005) 1-15
7. Wang P., Arabici G., and Pei D. Rapid sequencing of library-derived peptides by partial Edman degradation and mass spectrometry. J. Comb. Chem. 3 (2001) 251-254
8. Edman P., and Begg G. A protein sequenator. Eur. J. Biochem. 1 (1967) 80-91
9. Hewick R.M., Hunkapiller M.W., Hood L.E., and Dreyer W.J. A gas-liquid solid-phase peptide and protein sequenator. J. Biol. Chem. 256 (1981) 7990-7997
10. Chait B.T., Wang R., Beavis R.C., and Kent S.B.H. Protein ladder sequencing. Science 262 (1993) 89-92
11. Boyd V.L., Bozzini M., Zon G., Noble R.L., and Mattaliano R.J. Sequencing of peptides and proteins from the carboxyterminal. Anal. Biochem. 206 (1992) 344-352
12. Samyn B., Hardeman K., Van der Eycken J., and Van Beeumen J. Applicability of the alkylation chemistry for chemical C-terminal protein sequence analysis. Anal. Chem. 72 (2000) 1389-1399
13. Horn D.M., Zubarev R.A., and McLafferty F.W. Automated de novo sequencing of proteins by tandem high-resolution mass spectrometry. Proc. Natl. Acad. Sci. USA 97 (2000) 10313-10317
14. Syka J.E.P., Coon J.J., Schroeder M.J., Shabanowitz J., and Hunt D.F. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. USA 101 (2004) 9528-9533
15. Budnik B.A., Nielsen M.L., Olsen J.V., Haselmann K.F., Hörth P., Haehnel W., and Zubarev R.A. Can relative cleavage frequencies in peptides provide additional sequence information?. Intl. J. Mass Spectrom. 219 (2002) 283-294
16. Zong H., Zhang Y., Wen Z., and Li L. Protein sequencing by mass analysis of polypeptide ladders after controlled protein hydrolysis. Nat. Biotechnol. 22 (2004) 1291-1296
17. Patterson D.H., Tarr G.E., Regnier F.E., and Martin S.A. C-teminal ladder sequencing via matrix-assisted laser desorption mass spectrometry coupled with carboxypeptidase Y time-dependent and concentration-dependent digestions. Anal. Chem. 67 (1995) 3971-3978
18. Cool D.R., and Hardiman A. C-terminal sequencing of peptide hormones using carboxypeptidase Y and SELDI-TOF mass spectrometry. BioTechniques 36 (2004) 32-34
19. Huang R.H., Zhang Y., and Wang D.C. Primary structural determination of N-terminally blocked peptides from the bark of Eucommia ulmiodes Oliv by mass spectrometric analysis. Rapid Commun. Mass Spectrom. 17 (2003) 903-908
20. Hayashi R., Bai Y., and Hata T. Kinetic studies of carboxypeptidase Y. J. Biochem. 77 (1975) 69-79
21. Degal F.D., Rbedeau-Dumas B., and Breddam K. Purification and characterization of two serine carboxypeptidases from Aspergillus niger and their use in C-terminal sequencing of proteins and peptide synthesis. Appl. Environ. Microbiol. 58 (1992) 2144-2152
22. Klarskov K., Breddam K., and Roepstorff P. C-terminal sequence determination of peptides degraded with carboxypeptidases of different specificities and analyzed by 252-Cf plasma desorption mass spectrometry. Anal. Biochem. 180 (1989) 28-37
23. Thiede B., Wittmann-Liebold B., Bienert M., and Krause E. MALDI-MS for C-terminal sequence determination of peptides and proteins degraded by carboxypeptidase Y and P. FEBS Lett. 357 (1995) 65-69
24. Mortensen U.H., Stennicke H.R., Raaschou-Nielsen M., and Breddam K. Mechanistic study on carboxypeptidase Y-catalyzed transacylation reactions: Mutationally altered enzymes for peptide synthesis. J. Am. Chem. Soc. 116 (1994) 34-41
25. Mortensen U.H., Remington S.J., and Breddam K. Site-directed mutagenesis on (serine) carboxypeptidase Y: a hydrogen bond network stabilizes the transition state by interaction with the C-terminal carboxylate group. Biochemistry 33 (1994) 508-517