Post-translational modifications (PTM)
Using the basic protein identification as a platform, more complex data analysis can be performed to identify extra information that may be present on the protein e.g. post-translational modifications.
Under collision-induced dissociation (CID) conditions in the gas cell, peptides fragment to yield y- ion (carboxyl terminus) and b- ion (amino terminus) series with the mass difference between the two consecutive ions corresponding to the mass of an amino acid residue.
Phosphopeptides, like the example above, exhibit 'signatures' that are used to determine the presence of phosphorylation and also the specific residue location.
Phosphoserine and phosphothreonine residues normally undergo a constant neutral loss of phosphoric acid (H3PO4; 98 daltons) through CID in the gas phase. this neutral loss can be seen as the peak to the left of the doubly-charged precursor ion [M+2H]2+.
The mass difference between the precursor and the neutral loss signature is dependent on the charge state of the peptide. For example, the distance between the two peaks here is the mass-to-charge ratio (m/z) of 49 Da (98 Da / 2+ =49 Da).
Phosphotyrosine is more stable in the gas phase and therefore doesn't exhibit a neutral loss.
Peptide fragmentation can determine the exact location of the phosphorylation modification. The position of the modification can be localised by calculating the mass difference between two consecutive peaks within the ion series. in the example above, the mass difference between the y13 and y14 ions equates to 181 Da (threonine; 101 Da) with the addition of phosphate (80 Da).