New Developments in Targeted Analysis of Protein Posttranslational Modifications

Posttranslational modifications (PTMs) are dynamic regulators of protein function, and play important roles in diseases such as cancer. PTM analysis can be challenging, the stoichiometry of PTMs is often low, and various combinatorial modifications are possible. Currently, two major techniques are used to detect and characterize PTMs, immunoassays and mass spectrometry. Immunoassays rely on antibodies for detection of the protein of interest, and are therefore limited to targeted analysis. Mass spectrometry, on the other hand, is capable of characterizing posttranslational modifications both in targeted or non-targeted methods. Recently, new immunoassays were introduced that improve current methods, but also appear particularly promising in the analysis of PTMs. Two of these new immunoassays, proximity ligation assay and nanoscale immunoassay, are discussed in this review. In contrast to immunoassays, mass spectrometry enables characterization of a priori unknown PTM sites. A bottom-up approach, in which proteins are digested into smaller peptides, is well suited for targeted assays as well as cataloging PTMs. A top-down approach, where intact proteins are measured, is challenging but allows mapping of combinatorial PTMs. Mass spectrometry and immunoassays are therefore complementary techniques in analysis of PTMs. Advances in these methods now enable extremely sensitive detection of PTMs from very little material (immunoassays), or can fully characterize combinatorial modifications on proteins in both targeted and non-targeted ways (mass spectrometry). Recent developments in these techniques discussed in this review will therefore likely play an important role in current and future PTM analysis, particularly in the field of cancer research.