How to interpret modification sites in protein mass spectrometry
The modification of proteins plays an important role in biology, affecting the structure and function of proteins. By using mass spectrometry, we can analyze the modification sites of proteins.
1. Identification of Modification Sites
On a mass spectrum, modifications are usually reflected as mass shifts on specific residues. For example, phosphorylation modifications will increase the m/z value of the modified peptide by about 80 Da. This mass difference is due to the addition of a phosphate group. If you observe a mass difference in the mass spectrum, you can infer that a modification might have occurred. Then, you can further determine which residues might be modified under this mass difference. In the case of phosphorylation, possible modified residues are serine (S), threonine (T), and tyrosine (Y).
2. Localization of Modification Sites
The localization of modification sites primarily relies on the cleavage position within the peptide. For example, if a particular residue within a peptide is modified, two interconnected peaks (i.e., double peaks) will appear on the mass spectrum, caused by the residue, with the mass difference equal to the modification's mass. By finding such double peaks, the specific residue where the modification occurred can be determined.
1. Peptide AGpTP
Taking the peptide AGpTP as an example, where the T residue is phosphorylated. On the mass spectrum, we can see two peaks caused by T with a mass difference of 80 Da, indicating that the T residue has undergone phosphorylation.
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