The msms.txt file with the MaxQuant search results is a tab-separated text file that you can look at in Microsoft Excel.
When you choose a score cutoff of 0.99, BiblioSpec will not include rows where the value in the "PEP" column is greater than 0.01.
In theory, the FDR and PEP are quite different numbers. There is an explanation of the difference on page 2 of this document from the Noble lab:
When BiblioSpec is looking through your MaxQuant search results, BiblioSpec really is using the PEP number that MaxQuant provides. I am not sure whether the difference that you are seeing has something to do with the difference between FDR and PEP. It might be that there is a different set of numbers that you could be looking at in MaxQuant.
When you do an MSAmanda search in Skyline, I know that Percolator is used to assign the probabilities. I do not know whether those probabilities are FDR's or PEP's, but probably someone else on this support board can give you a better answer.
Can you send us an example of some MaxQuant results where the 0.99 cutoff was causing BiblioSpec to reject some matches that you did not think should be rejected? We might be able to figure out what is going on when we see your peptide search results. We do not have very much expertise with actually using MaxQuant, but some of the people on our team understand the file formats very well.
Files which are less than 50MB can be attached to this support request. You can upload larger files here: