Proteins are very often the subject of various post-translational modifications (PTMs) that can impact their association with other proteins and globally other biomolecules, their subcellular localization and their stability. Both the protein abundance and the levels of PTMs can vary between cellular states, such as cells submitted to an environmental stimulus or left otherwise, between differentiation states or between normal and diseased tissues.

The ProFI teams have developed expertise in the analysis of several types of PTMs, in particular phosphorylations, methylations, acetylations, O-glycosylations, and also in assessing the possible cleavage of protein N-termini to yield the mature sequences. The large-scale LC-MS/MS analysis of one type of PTM usually requires the enrichment of the proteolytic peptides bearing the PTM of interest, by implementing a step of affinity purification. Besides, some PTMs produce specific fragments that can be tracked in MS/MS to pinpoint peptide sequences containing the PTM of interest. The ProFI teams have been developing methods at the two levels to increase the specificity, sensitivity and thus coverage of the proteome bearing the above PTMs. PTMs investigations are also based on our strategies and instrumentation for large-scale and targeted quantification.