Analysis of PTMs

Many post-translational protein modifications (PTMs) can be identified by mass spectrometry. Modern high accuracy mass measurements give more confidence in the identification of these modifications. The resolution and mass accuracy of an Orbitrap instrument enables us to distinguish between phosphorylation vs sufation (delta mass of 0.0095), tri-methylation vs acetylation (delta mass of 0.036) or deamidation vs the 13C peak of the unmodified form (delta mass of 0.019) etc.

In general a single protein species is differentially modified i.e. each modification may occur in different ratios and at different sites which complicates the analysis. The abundance of tryptic peptides containing PTMs is therefore lower than the abundance of tryptic peptides that never gets modified. Finding a particular PTM is sometimes as difficult as fining a needle in a haystack and often involves time-consuming manual interpretation of LC-MS/MS data.