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.