Hi Brett,

Would you mind emailing me the msms.txt and mqpar.xml file?

Thanks,
Kaipo

I'm not sure what's going on here - we would expect to see a modification in the "Modifications" column for that particular line, but the value is "Unmodified".

Unfortunately we need to have the modification listed in the Modifications column, because the two letter abbreviations are often ambiguous (as in this case). "de" could be "Deamidation (N)", "Deamidation 180 (N)", or "Deamidation (NQ)".

My guess is that this is a bug in MaxQuant, so you may want to contact MaxQuant support. But if you don't mind manually editing the msms.txt file, you can replace "Unmodified" with the title of the modification (e.g. "Deamidation (N)"). That should allow the library builder to figure out what it is.

Thanks,
Kaipo

I am also getting the same problem: trying to upload the msms.txt file , and receiving a similar error message for phosphorylation. Is there a solution ? (couldn't find one on the support page).
And a related question: the cutoff field in library building relates to which column in the Maxquant scoring ?

best regards, Ariel

Hi Ariel,

This is still a mystery to me (why there are modifications in a peptide sequence but the Modifications column value is "Unmodified") which I am trying to find the answer to.

In the msms.txt files, the cutoff score applies to the PEP column.

Thanks,
Kaipo

It seems like a writing error from MaxQuant. For example peptide xxx(ox)xxx will have the Modified Sequence but under the Oxidation column it will say 0 and under the 'Modifications' column it will say "Unmodified". Best way is to basically put "1" in the specific modification column (ie 1, 2, or 3 etc... depending on the number of times peptide is modified by the same modification, so for xxx(ox)xxx you would put 1 under the Oxidation (M) column) and under the modification column put in the correct name (ie. 'Oxidation (M)' ) .

When you get the error it will say which line the error is occurring at. Basically open the msms.txt with excel, freeze the top row, and find the line error is occurring at and fix it. It's a bit annoying but it doesn't happen that often, for example in a 500 mg msms file (~300,000 lines) for me it happened 4 times. You can alternatively just delete the whole line but I didn't try that. I'll see if I can let the MaxQuant people be aware of the error somehow.

Cheers,

T

Just got some feedback. It has to do with second peptide search in MaxQuant, it's an error in that it's reporting the wrong sequence (second best) instead of the best one. So best suggestion I got was just to delete it.

Thanks for the help figuring out this issue Tanveer. I suppose we should automatically skip such lines when building a library.

Kaipo