Abstract
Mass spectrometry (MS) is one of the most powerful techniques at hand to investigate the protein players in biological systems. In fact, the number of studies involving molecular MS techniques, e.g. matrix-assisted laser desorption/ionisation (MALDI)-MS or electrospray ionisation (ESI)-MS, in the field of proteomics has rocketed in recent years [1, 2]. In any case, today’s proteomics platform is built on technologies to identify large numbers of proteins in the same experiment. Characterization of such huge numbers of peptides and proteins in real-life complex mixtures, resulting from bottom-up or top-down proteomic strategies, is a rather difficult and intricate task. Notwithstanding its present worldwide use, the great difficulties encountered could explain why proteomics results so far have been mainly qualitative in nature [3]. The need for quantitative approaches and data, however, cannot be overemphasised today: they are essential to obtain more precise information on the function of proteins, their temporal changes in the proteome, the kinetics of such changes, etc., allowing sound models to be established that are able to shed more light on the fundamental and cooperative roles of proteins in biological systems. In this vein, Ong and Mann recently published a seminal paper whose title, “MS-based proteomics turns quantitative” [3], stresses the new trend. The slow progress of quantitation in proteomics stems from the extreme difficulties associated with the accurate and precise determination of the absolute amount of a given protein in a complex mixture containing many other proteins and varied biocompounds. The main drawbacks making “quantitative” proteomics a tough challenge include:
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