G PTM D: Global Post translational Modification Discovery Task

G-PTM-D is a tool used to expand the scope of peptide identification to include specific post-translational modifications. Currently, identifying peptides with post-translational modifications relies on the variable toggling of modifications on all the residues that can be modified or the documentation of a specific modification in a database. The first method is computationally expensive and wasteful while databases are often incomplete. Thus, G-PTM-D addresses the weaknesses of both methods to improve protein identification results.

The purpose of G-PTM-D is to build a new proteome reference .xml database by annotating an existing reference database using a set of peptide spectral matches (PSMs). The PSMs are obtained by running a MetaMorpheus search on a .raw or .mzml file of the experimentally obtained mass spectrometry data. The program identifies the peptide spectral matches that have a mass shift indicative of certain post-translational modifications or substitutions. For example, if the peptide “PEPTIDE” was identified in the PSMs file with a mass shift of 79.966 Da, the corresponding protein entry in the reference .xml database would be granted a new feature consisting of a phosphorylated threonine at the appropriate position because 79.966 Da is exactly the change in mass of a peptide when one residue is phosphorylated.

Now, when the original .raw or .mzml file is run against this new database in an open search, if the phosphorylation on the threonine is present in the sample, the computer will be able to recognize and identify it. Phosphorylation is just one example, and this technique extends to other post-translational modifications. The user can add or remove modifications to the list of post-translational modifications as needed. This effectively allows for variable post-translational modifications at targeted positions in the protein leading to better search results upon the second pass without incurring huge data costs associated with blindly adding variable modifications.