Quantitation of target proteins and post-translational modifications in affinity-based proteomics approaches

As proteomics attempts to enter clinical and diagnostic application, key issues surrounding the viability of various proteomics approaches must be evaluated. A major issue at the forefront of discussion is the ability to quantitate protein targets, including the discrimination of endogenous variants that are the result of genetic and post-translational modifications. Mass spectrometry is the logical solution to this problem because of its ability to capitalize on the intrinsic property of molecular mass. However, the ability to successfully compete with classical immunoassays, the dominant technologies in the clinical and diagnostic world for quantitative protein assessment, is not a trivial task. This review offers a comprehensive discussion regarding some of the major developments in quantitative approaches towards both top-down and bottom-up proteomics. Described in more detail is the mass spectrometric immunoassay, including examples of how immunoaffinity capture is enhanced with mass spectrometry detection, and the use of this approach in protein quantification may be viewed as an improvement of the currently accepted clinical and diagnostic methodologies.