Mass Spectrometry in Protein Characterization


The complete complement of proteins in a cell, the proteome, is highly complex because a single protein can exist in several different forms. Mass spectrometry has emerged as the tool of choice for protein identification as well as for characterization of posttranslational modifications.

Keywords: mass spectrometry; ionization; posttranslational; modifications; phosphorylation; quantification; MALDI


Bennett KL, Matthiesen T and Roepstorff P (2000) Probing protein surface topology by chemical surface labeling, crosslinking, and mass spectrometry. Methods in Molecular Biology 146: 113–132.

Goshe MB, Conrads TP, Panisko EA, et al. (2001) Phosphoprotein isotope‐coded affinity tag approach for isolating and quantitating phosphopeptides in proteome‐wide analyses. Analytical Chemistry 73: 2578–2586.

Gygi SP, Rist B, Gerber SA, et al. (1999) Quantitative analysis of complex protein mixtures using isotope‐coded affinity tags. Nature Biotechnology 17: 994–999.

Hernandez H and Robinson CV (2001) Dynamic protein complexes: insights from mass spectrometry. Journal of Biological Chemistry 276: 46685–46 688.

Horn DM, Zubarev RA and McLafferty FW (2000) Automated de novo sequencing of proteins by tandem high‐resolution mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America 97: 10313–10317.

Laiko VV, Moyer SC and Cotter RJ (2000) Atmospheric pressure MALDI/ion trap mass spectrometry. Analytical Chemistry 72: 5239–5243.

Loboda AV, Krutchinsky AN, Bromirski M, Ens W and Standing KG (2000) A tandem quadrupole/time‐of‐flight mass spectrometer with a matrix‐assisted laser desorption/ionization source: design and performance. Rapid Communications in Mass Spectrometry 14: 1047–1057.

Oda Y, Huang K, Cross FR, Cowburn D and Chait BT (1999) Accurate quantitation of protein expression and site‐specific phosphorylation. Proceedings of the National Academy of Sciences of the United States of America 96: 6591–6596.

Oda Y, Nagasu T and Chait BT (2001) Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nature Biotechnology 19: 379–382.

Shevchenko A, Wilm M and Mann M (1997) Peptide sequencing by mass spectrometry for homology searches and cloning of genes. Journal of Protein Chemistry 16: 481–490.

Vestal ML (2001) Methods of ion generation. Chemical Reviews 101: 361–375.

Washburn MP, Wolters D and Yates JR III (2001) Large‐scale analysis of the yeast proteome by multidimensional protein identification technology. Nature Biotechnology 19: 242–247.

Weckwerth W, Willmitzer L and Fiehn O (2000) Comparative quantification and identification of phosphoproteins using stable isotope labeling and liquid chromatography/mass spectrometry. Rapid Communications in Mass Spectrometry 14: 1677–1681.

Wilm M and Mann M (1996) Analytical properties of the nanoelectrospray ion source. Analytical Chemistry 68: 1–8.

Yamashita M and Fenn JB (1984) Electrospray ion source. Another variation on the free‐jet theme. Journal of Physical Chemistry 88: 4451–4459.

Zhou H, Watts JD and Aebersold R (2001) A systematic approach to the analysis of protein phosphorylation. Nature Biotechnology 19: 375–378.

Further Reading

Aebersold R and Goodlett DR (2001) Mass spectrometry in proteomics. Chemical Reviews 101: 269–296.

Burlingame AL, Carr SA and Baldwin MA (eds.) (2000) Mass Spectrometry in Biology and Medicine. Totowa, NJ: Humana Press.

Chapman JR (ed.) (2000) Mass Spectrometry of Proteins and Peptides. Totowa, NJ: Humana Press.

Larsen MR and Roepstorff P (2000) Mass spectrometric identification of proteins and characterization of their post‐translational modifications in proteome analysis. Fresenius Journal of Analytical Chemistry 366: 677–690.

Mann M, Hendrickson RC and Pandey A (2001) Analysis of proteins and proteomes by mass spectrometry. Annual Reviews of Biochemistry 70: 437–473.

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Steen, Hanno, and Pandey, Akhilesh(Jan 2006) Mass Spectrometry in Protein Characterization. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1038/npg.els.0005726]