Mayu parsing TPP output

[Kris]

Hi,

I was hoping someone might know why my Mayu software won't work. I
have been using Mayu on .pep.xml output from TPP with a fasta file
that includes Decoy sequences.

The Mayu software appears to successfully read the fasta file.
However, I believe it can't parse the pepxml output properly (even
though I'm specifying TPP pepxml output with the command). It tells me
either the file is poor or no data was specified.

Should I be using peptide prophet output files instead of peptide
prophet input files?

Should I add something to the Mayu software, so that it can
successfully parse the TPP pepxml format?

I don't really understand why it doesn't work. The files get
successfully parsed in the TPP Analyze Peptide (peptide prophet).

Any help would be appreciated.

-Kris