Modern strategies for protein quantification in proteome analysis: advantages and limitations

Over the last 3 years, a number of mass spectrometry-based methods for the simultaneous identification and quantification of individual proteins within complex mixtures have been reported. Most, if not all, of such strategies apply a two-step approach: the first for the separation of proteins or peptides, and the second uses mass spectrometry to identify and quantify the individual components. To simplify the outcome of both steps, certain chemicals and heavy-isotope-labeling are commonly used in the early stages of sample preparation (except in differential fluorescence labeling protocols). The ultimate goal of these strategies is to be able to identify every protein expressed in a cell or tissue, and to determine each protein's abundance, state of modification, and possible involvement in multi-protein complexes. In this review, an attempt is made to highlight the salient characteristics of the existing strategies with particular attention to their strengths and weaknesses.