Chemistry in Proteomics: An Interplay between Classical Methods in Chemical Modification of Proteins and Mass Spectrometry at the Cutting Edge

This review deals with chemical approaches that facilitate proteomics research. The methods include chemical cleavage of peptide bonds, stepwise degradation of proteins, and site-specific modification enabling the discrimination between functional groups. These reactions could enhance the efficacy of mass spectrometry (MS) for identification, quantification, and sequencing of peptides and proteins. Particular stress is laid on the effect of each modification on mass spectra mainly with respect to the enhancement of peak intensities, the clarity of spectra, and the suppression of ambiguity in peak assignment. Chemical modifications targeting the terminal free amino and carboxyl groups are reviewed, because the charge or isotopic tagging on N- and C- termini has proved effective to identify a protein based on the terminal amino acid sequencing with tandem MS in combination with database searching. Such a tag that is designed to provide a peak with a characteristic sensitivity or pattern could corroborate the implication of mass spectra and facilitate the de novo protein sequencing of mature proteins, which are often subjected to post-translational modifications.