Add line to mzid output?

[lin...@uw.edu]

Hello MSAmanda Team,

I am trying to parse the mzid output of MSAmanda via Pyteomics. I noticed that Pyteomics interprets every single PSM in the output as a decoy PSM. This occurs because Pyteomics uses a certain field in the output that does not exist in the mzid that MSAmanda outputs.

Specifically, is it missing the field with the name of "decoy DB accession regexp".

Below is an example of what I mean.

<DatabaseName>
<userParam name="ecoli.fasta"/>
</DatabaseName>
<cvParam cvRef="PSI-MS" accession="MS:1001283" name="decoy DB accession regexp" value="^XXX"/>

....

Below is what I see in the MSAmanda mzid output.

<DatabaseName>
<userParam name="ecoli.fasta" />
</DatabaseName>
<cvParam name="database type amino acid" cvRef="PSI-MS" accession="MS:1001073" />

....

Would it be possible to add the "decoy DB accession regexp" field?

Thank you,

Andy

[Viktoria Dorfer]

Hi Andy,

sorry for the late reply, that message somehow got lost...So you would expect the value to be "^REV_" as decoy proteins are marked with that flag in MS Amanda?

Thanks!

Best regards,

Viktoria