This is an old post but I thought may be you could help me. I have Proteome
Discoverer v2.0 exported pep.xml and it is not working with PeptideProphet.
How did you analyze your results with PeptideProphet?
Thank you very much,
On Wednesday, August 19, 2015 at 1:54:13 PM UTC-4, waovoo wrote:
> I cannot create spectral library when I use the merged mzXML and pep.xml
> file generated from multiple raw files on PD1.4.
> For example, there are two raw files, A.raw and B.raw. I analyzed this
> two raw files with Proteome Discoverer 1.4 (PD1.4) all together to generate
> one merged files, All.mzML file and All.msf file. This All.mzML file was
> converted to All.mzXML file by MSConvert. All.msf file was used to export
> All.pep.xml file on PD1.4. In All.pep.xml file, I replaced percolator and
> percolator_result with peptideprofet and peptideprofet_result,
> respectively. Finally, I tried to create spectral library from All.pep.xml
> file and All.mzXML file by using prompt command of SpectraST on Windows,
> but it didn't work.
> I successfully created a library when I processed two raw files
> separately. So, when I use merged files generated from multiple raw data on
> PD1.4, there are some problems.
> Is there any way to solve this problem?
> Thank you.
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