I'm at the end of a multi-year odyssey of a project, and I just need to submit data to PRIDE.
Unfortunately, when I run tpp2mzid for some prot.xml files, I get an error such as this: Warning (A), no peptide evidence found for (mod): EENAFVQKIAE from Br20418.t2 This only happens for some prot.xml files, but I'm not sure why. The pep.xml files from which the prot.xml are derived convert fine. I've put an example here: https://we.tl/t-Z9qNNjDC0k I was running TPP via the docker container: digitalproteomes/tpp:version-5.2.0.1 Here is the stdout in full: Reading: HCLC_EhN.prot.xml Reading: /data/HCLC_EhN_ipro.pep.xml Unknown xx modification: B = 114.535 42.5515 Unknown xx modification: J = 113.084 44.0023 Unknown xx modification: O = 237.148 80.0613 Unknown xx modification: U = 150.954 6.13277 Unknown xx modification: X = 111 46.0864 Unknown xx modification: Z = 128.551 28.5358 Unknown xx modification: B = 114.535 42.5515 Unknown xx modification: J = 113.084 44.0023 Unknown xx modification: O = 237.148 80.0613 Unknown xx modification: U = 150.954 6.13277 Unknown xx modification: X = 111 46.0864 Unknown xx modification: Z = 128.551 28.5358 Unknown xx modification: B = 114.535 42.5515 Unknown xx modification: J = 113.084 44.0023 Unknown xx modification: O = 237.148 80.0613 Unknown xx modification: U = 150.954 6.13277 Unknown xx modification: X = 111 46.0864 Unknown xx modification: Z = 128.551 28.5358 Unknown xx modification: B = 114.535 42.5515 Unknown xx modification: J = 113.084 44.0023 Unknown xx modification: O = 237.148 80.0613 Unknown xx modification: U = 150.954 6.13277 Unknown xx modification: X = 111 46.0864 Unknown xx modification: Z = 128.551 28.5358 Unknown xx modification: B = 114.535 42.5515 Unknown xx modification: J = 113.084 44.0023 Unknown xx modification: O = 237.148 80.0613 Unknown xx modification: U = 150.954 6.13277 Unknown xx modification: X = 111 46.0864 Unknown xx modification: Z = 128.551 28.5358 Unknown xx modification: B = 114.535 42.5515 Unknown xx modification: J = 113.084 44.0023 Unknown xx modification: O = 237.148 80.0613 Unknown xx modification: U = 150.954 6.13277 Unknown xx modification: X = 111 46.0864 Unknown xx modification: Z = 128.551 28.5358 Unknown xx modification: B = 114.535 42.5515 Unknown xx modification: J = 113.084 44.0023 Unknown xx modification: O = 237.148 80.0613 Unknown xx modification: U = 150.954 6.13277 Unknown xx modification: X = 111 46.0864 Unknown xx modification: Z = 128.551 28.5358 Unknown xx modification: B = 114.535 42.5515 Unknown xx modification: J = 113.084 44.0023 Unknown xx modification: O = 237.148 80.0613 Unknown xx modification: U = 150.954 6.13277 Unknown xx modification: X = 111 46.0864 Unknown xx modification: Z = 128.551 28.5358 17648 psms read. Warning (A), no peptide evidence found for (mod): EENAFVQKIAE from Br20418.t2 Help would be very much appreciated! Thanks, Alastair -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/f3791dbe-d3d4-43cf-aeda-65792741656fn%40googlegroups.com.
