Protein sequencing by mass analysis of polypeptide ladders after controlled protein hydrolysis

Nature Biotechnology

Volumn 22, Issue 10, 2004, Pages 1291-1296

  Zhong, Hongying ^a   Zhang, Ying ^a   Wen, Zhihui ^a   Li, Liang ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CELLS; ESCHERICHIA COLI; GENES; HYDROLYSIS; IRRADIATION; MASS SPECTROMETRY; MICROWAVES; PROTEINS;

MICROWAVE IRRADIATION; POLYPEPTIDE LADDERS; PROTEIN ANNOTATION;

POLYPEPTIDES;

POLYPEPTIDE; PROTEIN;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; ESCHERICHIA COLI K 12; MASS SPECTROMETRY; MICROWAVE IRRADIATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN HYDROLYSIS; PROTEIN ISOLATION; PROTEIN MODIFICATION; PROTEIN PHOSPHORYLATION; SEQUENCE ANALYSIS; VALIDATION PROCESS;

ALGORITHMS; AMINO ACID SEQUENCE; AMINO ACIDS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; HYDROLYSIS; MASS SPECTROMETRY; MICROWAVES; MOLECULAR SEQUENCE DATA; PROTEIN PROCESSING, POST-TRANSLATIONAL; SEQUENCE ANALYSIS, PROTEIN;

ESCHERICHIA COLI; ESCHERICHIA COLI K12;

EID: 5044222901     PISSN: 10870156     EISSN: None     Source Type: Journal    
DOI: 10.1038/nbt1011     Document Type: Article

References (30)

1. Hunt, D.F. et al. Characterization of peptides bound to the class I MHC molecule HLA-A2.1 by mass spectrometry. Science 255, 1261-1263 (1992).
2. Hinter, M. & Sherman, N.E. Protein Sequencing and Identification Using Tandem Mass Spectrometry. (Wiley, New York, 2000).
3. Kelleher, N.L. et al. Top down versus bottom up protein characterization by tandem high resolution mass spectrometry, J. Am. Chem. Soc. 121, 806-812 (1999).
4. Sze, S.K., Ge, Y., Oh, H. & McLafferty, F.W. From the cover: Top-down mass spectrometry of a 29-kDa protein for characterization of any post-translational modification to within one residue. Proc. Natl. Acad. Sci. USA 99, 1774-1779 (2002).
5. Patterson, D.H., Tarr, G.E., Regnier, F.E. & Martin, S.A. C-terminal ladder sequencing via matrix-assisted laser desorption mass spectrometry coupled with carboxypeptidase Y time-dependent and concentration-dependent digestions. Anal. Chem. 67, 3971-3978 (1995).
6. Chait, B.T., Wang, R., Beavis, R.C. & Kent, S.B.H. Protein ladder sequencing. Science 262, 89-92 (1993).
7. Tsugita, A., Takamoto, K., Kamo, M. & Iwadate, H. C-terminal sequencing of protein. Eur. J. Biochem. 206, 691-696 (1992).
8. Vorm, O. & Roepstorff, P. Peptide sequence information derived by partial acid hydrolysis and matrix-assisted laser desorption/ionization mass spectrometry. Biol. Mass Spectmm. 23, 734-740 (1994).
9. Zubarev, R.A., Chivanov, V.D., Hakansson, P. & Sundqvist, B.U.R. Peptide sequencing by partial acid hydrolysis and high resolution plasma desporption mass spectrometry. Rapid Commun. Mass Spectrom. 8, 906-912 (1994).
10. Gobom, J., Mirgorodskaya, E., Nordhoff, E., Hojrup, P. & Roepstorff, P, Use of vaporphase acid hydrolysis for mass spectrometric peptide mapping and protein identification. Anal. Chem. 71, 919-927 (1999).
11. Shevchenko, A., Loboda, A., Shevchenko, A., Ens, W. & Standing, K.G. MALDI quadrupole time-of-flight mass spectrometry: a powerful tool for proteomic research. Anal. Chem. 72, 2132-2141 (2000).
12. Lin, S.H., Tornatore, P. & Weinberger, S.R. Limited acid hydrolysis as a means of fragmenting proteins isolated upon ProteinChip Array surfaces. Eur. J. Mass Spectrom. 7, 131-141 (2001).
13. Reiber, D.C., Brown, R.S., Weinberger, S., Kenny, J. & Bailey, J. Unknown peptide sequencing using matrix-assisted laser desorption/ionization and in-source decay. Anal. Chem. 70, 1214-1222 (1998).
14. Lennon, J.J. & Walsh, K.A. Direct sequence analysis of proteins by in-source fragmentation during delayed ion extraction. Protein Sci. 6, 2446-2453 (1997).
15. Keough, T., Youngquist, R.S. & Lacey, M.P. A method for high-sensitivity peptide sequencing using postsource decay matrix-assisted laser desorption ionization mass spectrometry. Proc. Natl. Acad. Sci. USA 96, 7131-7136 (1999).
16. Shevchenko, A. et. al. Rapid de novo peptide sequencing by a combination of nanoelectrospray, isotopic labeling and a quadrupole/time-of-flight mass spectrometer. Rapid Commun. Mass Spectmm. 11, 1015-1024 (1997).
17. Hillenkamp, F., Karas, M., Beavis, R.C. & Chait, B.T. Matrix-assisted laser desorption/ionization mass spectrometry of biopolymers. Anal. Chem. 63, 1193A-1203A (1991).
18. Whittal, R.M., Keller, B.O. & Li, L. Nanoliter chemistry combined with mass spectrometry for peptide mapping of proteins from single mammalian cell lysates. Anal. Chem. 70, 5344-5347 (1998).
19. Solouki, T., Marto, J.A., White, P.M., Guan, S. & Marshall, A.G. Attomole biomolecule mass analysis by matrix-assisted laser desorption/ ionization Fourier Transform ion cyclotron resonance. Anal. Chem. 67, 4139-4144 (1995).
20. Graves, D.J., Martin, B.L. & Wang, J.H. Co- and Post-translational Modification of Proteins (Oxford, New York, 1994).
21. Jones, J.J., Stump, M.J., Fleming, R.C., Lay, J.O. & Wilkins, C.L. Investigation of MALDI-TOF and FT-MS techniques for analysis of Escherichia coli whole cells. Anal. Chem. 75, 1340-1347 (2003).
22. Krutchinsky, A.N. et al. Orthogonal injection of matrix-assisted laser desorption/ionization ions into a time-of-flight spectrometer through a collisional damping interface. Rapid Commun. Mass Spectrom. 12, 508-518 (1998).
23. Loboda, A.V., Ackloo, S. & Chernushevich, I.V. A high-performance matrix-assisted laser desorption/ionization orthogonal time-of-flight mass spectrometer with collisional cooling. Rapid Commun. Mass Spectrom. 17, 2508-2516 (2003).
24. Schriemer, D.C. & Li, L. Mass discrimination in the analysis of polydisperse polymers by MALDI time-of-flight mass spectrometry. 1. Sample preparation and desorption/ionization issues. Anal. Chem. 69, 4169-4175 (1997).
25. Schriemer, D.C. & Li, L. Mass discrimination in the analysis of polydisperse polymers by MALDI time-of-flight mass spectrometry. 2. Instrumental issues. Anal. Chem. 69, 4176-4183 (1997).
26. st ASMS Conf. Mass Spectrometry and Allied Topics, 621 San Francisco, CA, May 31-June 4 1993.
27. Zhang, N., Doucette, A. & Li, L. Two-layer sample preparation method for MALDI mass spectrometric analysis of protein and peptide samples containing sodium dodecyl sulfate. Anal. Chem. 73, 2968-2975 (2001).
28. Zhang, N. & Li, L. Effects of common surfactants on protein digestion and MALDI MS analysis of the digested peptides using two-layer sample preparation. Rapid Commun. Mass Spectrom. 18, 889-896 (2004).
29. Nielen, M.W.F. MALDI time-of-flight mass spectrometry of synthetic polymers. Mass Spectrom. Rev. 18, 309-344 (1999).
30. Dai, Y., Whittal, R.M. & Li, L. Two-layer sample preparation: a method for MALDI-MS analysis of complex peptide and protein mixtures. Anal. Chem. 71, 1087-1091 (1999).