Exclude peptide terminus from variable modification

[marhartl]

Dear FragPipe team,

I am trying to avoid that certain variable modifications are assigned to an amino acid at a peptide C-terminus but as far as I can tell this cannot be defined in FragPipe. To give an example why this would be helpful: acetylated lysine cannot be cleaved by trypsin which means peptide C-terminal acetylated lysines should actually not occur. Similarly, this holds true for other lysine modifications, like for example ubiquitination.
With current FragPipe configuration I obtain peptides with C-terminally modified lysines, which need to be filtered out because they are obviously incorrect.

For this reason it would be great to be able to define a modification on a specific amino acid but which is NOT peptide C-terminal (or N-terminal if one wishes so).

Many thanks,
Markus

[anesvi]

This is a good suggestion, and we discussed adding it before but did not implement it yet.

[SaschaVatic]

.

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On Mon, Jan 20, 2025 at 2:18 PM Alexey Nesvizhskii ***@***.***> wrote: This is a good suggestion, and we discussed adding it before but did not implement it yet. — Reply to this email directly, view it on GitHub <#1989 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BNTON4XEENM2PXWJENGWC2D2LTZQVAVCNFSM6AAAAABVP4YYP6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMBSGQYDMOJSHE> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>