PTM with no unimod ID

[BrBella]

Dear Vadim,
first, thank you for developing this great tool.
I have an error caused by a modification in my DDA based library: a modification that was added in the fragpipe search does not have unimod ID (this is homocysteinylation).
Is there any way to still add this to the search?
Even if I used the strip unknown mod command, I have the same problem.
Thanks and best,Bella

[vdemichev]

Hi Bella,

Yes, please just declare it with --mod.

Best,
Vadim

[BrBella]

Thank you! It seems that the modification is now recognized.
Regarding the modifications, I saw that out of the 7-8 modifications in my library, only the first 5 will be searched for.
Is it possible to increase that number?

[vdemichev]

Only 5 will be localised, this is a technical limitation at the moment. Although I don't think it's a problem (I cannot think of a biological scenario where you'll have more than 5 distinct modifications that require localisation, i.e. even if sth like various variable mods on histone lysines, it's not like it's really important to localise those as it's usually a single lysine).

Best,
Vadim