Hi,

I am trying to use CPAS and Xpress for the analysis of a metabolically labeled sample. The sample is a mix between 14N-labeled peptides and 15N-labeled peptides. The parameters I use for the search of 15N-labeled peptides are:

<?xml version="1.0" encoding="UTF-8"?>
<bioml>
    <note label="protein, cleavage site" type="input">[KR]|{P}</note>
    <note label="protein, modified residue mass file" type="input">C:\Inetpub\wwwroot\ISB\data\parameters\n15.xml</note>
    <note label="pipeline quantitation, algorithm" type="input">xpress</note>
    <note label="pipeline quantitation, metabolic search type" type="input">heavy</note>
    <!-- Override default parameters here. -->
    <note label="pipeline, database" type="input">TAIR9_pep_20090619.fasta</note>
</bioml>

I then repeat the search for the same sample changing the parameters to consider 14N-labeled peptides that are picked up by the mass spec. Is there a way to combine these two searches and to get one final protXML file. Or does this have to be done outside of CPAS using interprophet?

Thanks,

Maik