Exercise MSMS7: answers
- How can you distinguish between peak picking choosing the 13C peak and deamidation?
If you have low ppm accuracy, you can tell from the precursor mass. 13C is 1.0033 Da heavier than 12C while deamidation is 0.984 Da. For a peptide of mass 1800 Da, these differ by 11 ppm.
If you don’t have this accuracy, it may be possible to tell from the fragment matches. If the peptide is deamidated, but you match it without this modification by allowing a precursor mass error of 1 Da, fragments containing the deamidated residue will not be matched. Exactly the same applies if the precursor is actually 13C, but a match is obtained by introducing a false deamidation. Only the "correct" match will give fragment matches spanning the deamidation site(s). Of course, this can be difficult to spot this unless you have extensive fragmentation in both C-terminal and N-terminal ion series.
- Is there evidence of non-specific cleavage?
Yes, an unusually high level of semi-specific peptides. Try using semi-trypsin as the enzyme or an error tolerant search