ERROR: illegal character _ found in sequence [xxxxxxxx].... (line xxx)

ERROR: illegal character _ found in sequence [xxxxxxxx].... (line xxx) siljebt  2020-07-26

I´m experiencing a problem using MaxQuant v1.6.14 and Skyline v20.1.0.155, trying to build a library in Skyline using msms.txt files from MQ. The message I get states "ERROR: illegal character _ found in sequence [ ].... (line xxx)". I see that the message refers to a "_", but I cannot find it.

Skyline import /was/ working nicely with the most conventional PTMs (oxidation, carboxylation, etc), but when I built on with additional PTMs in my MQ search the problem arose. It at first seemed like the problem arises when deamidation and amidation occur in the same peptide, but after manually deleting the lines that are causing problems - one by one, it seems like my initial assumtions about the cause for the error is not the case.

Brendan MacLean responded:  2020-07-26

The problem is how a C-terminal modification is represented. R_(

I think you could probably get past it with a Find and Replace of R_( with R( and K_( with K(

We should fix this of course, but that may be all you need to get what you want.

Thanks for report the issue.


siljebt responded:  2020-07-26

Dear Brendan,
Thank you for the fast and usefull response. It does not seem to give the error for all cases of R_( as I have that in my first line), but it indeed occurs when there is a C-term modification, as you stated. The replace all command did the trick.
Thank you again,