Abstract
Bottom-up proteomics is the analysis of peptides derived from single proteins or protein mixtures, and because each protein generates tens of peptides, there is scope for controlled reduction in complexity. We report here a new strategy for selective isolation of the N-terminal peptides of a protein mixture, yielding positionally defined peptides. The method is tolerant of several fragmentation methods, and the databases that must be searched are substantially less complex.
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References
Bogdanov, B. & Smith, R.D. Mass Spectrom. Rev. 24, 168–200 (2004).
Standing, K.G. Curr. Opin. Struct. Biol. 13, 595–601 (2003).
Steen, H. & Mann, M. Nat. Rev. Mol. Cell Biol. 5, 699–711 (2004).
Smolka, M.B., Zhou, H., Purkayastha, S. & Aebersold, R. Anal. Biochem. 297, 25–31 (2001).
Kasai, K. J. Chromatogr. 597, 3–18 (1992).
Sechi, S. & Chait, B.T. Anal. Chem. 72, 3374–3378 (2000).
Yamaguchi, M. et al. Anal. Chem. 77, 645–651 (2005).
Chelius, D. & Shaler, T.A. Bioconjug. Chem. 14, 205–211 (2003).
Gevaert, K. et al. Nat. Biotechnol. 21, 566–569 (2003).
Martens, L. et al. Proteomics 5, 3193–3204 (2005).
Kuhn, K. et al. J. Proteome Res. 2, 598–609 (2003).
Kuhn, K. et al. Proteomics 5, 2364–2368 (2005).
Doherty, M.K., Whitehead, C., McCormack, H., Gaskell, S.J. & Beynon, R.J. Proteomics 5, 522–533 (2005).
Doherty, M.K. et al. Proteomics 4, 2082–2093 (2004).
Hayter, J.R., Robertson, D.H., Gaskell, S.J. & Beynon, R.J. Mol. Cell. Proteomics 2, 85–95 (2003).
Acknowledgements
Supported by grants to R.J.B. & J.L.H. from the Natural Environment Research Council and the Biotechnology and Biological Sciences Research Council. We are grateful to M. Doherty for assistance with the mass spectrometry.
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Supplementary information
Supplementary Fig. 1
Analysis of N-terminal peptides from mouse skeletal muscle. (PDF 118 kb)
Supplementary Fig. 2
Analysis of N-terminal enriched fraction from mouse liver soluble proteins. (PDF 126 kb)
Supplementary Fig. 3
Theoretical analysis of N-terminal positional peptides from mouse. (PDF 182 kb)
Supplementary Table 1
Identification of proteins in mouse liver from N-terminal peptides. (PDF 163 kb)
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McDonald, L., Robertson, D., Hurst, J. et al. Positional proteomics: selective recovery and analysis of N-terminal proteolytic peptides. Nat Methods 2, 955–957 (2005). https://doi.org/10.1038/nmeth811
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DOI: https://doi.org/10.1038/nmeth811
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