Some N-terminal acetylations are not N-terminal

[ndtivendale]

Protein N-terminal acetylation was included in my search as a variable modification. For most of the psms, the N-terminal acetylation is mapped to the first or second residue of the protein, which makes sense since I checked the box to 'Clip N-term M.' However I am finding a small number of psms with 'N-terminal' aceylations that are not mapped to the first or second residue of the protein. If these peptides are not mapped to the N-terminal end of their proteins, how can they be N-terminally acetylated? Why is this happening and how can I stop it? You can see the problem in the attached example output file.
Note, that I used '[^' to specify protein N-terminal acetylation in MSFragger.

psm_000_1.xlsx

[ndtivendale]

I am not sure why that text came out so big! Sorry.

[fcyu]

Seems to be the same one as #718

Can you check if those peptides can be mapped to another protein, which makes it N-term Acetylation?

Best,

Fengchao