Cannot import iProphet pepXML file to build a spectral library

Cannot import iProphet pepXML file to build a spectral library marc isaksson  2019-09-24


I tried to generate a library in Skyline from an iProphet pepXML file, but failed in the last step.

Long story short:

I tried to create it the library by first starting a blank document. Then I went to Settings>Peptide Settings and clicked on the Library tab.
I entered all info regarding file names, output path for library, cut-off score and what iRT peptides I used.

In the next step, I added the iProphet pepXML file, and then clicked on the Finish Button. After a few seconds, the software threw an error. It seems like Skyline/BlibBuild cannot find an attribute called SpectrumNativeID in the iProphet pepXML?


FYI: I made sure to copy the iProphet.pep.xml file into the same directory(Working directory: D:\Data_TPP\RAW_files) as the mzML files used for the database searching (combined both Comet and X!Tandem searches into a single iProphet file).

I used the TPP v.5.0.2, with X!Tandem (old: Jackhammer 2013.06.15.1) and Comet (v.2018.01 rev.4).

If you could help me solve this issue, I would be really happy.



marc isaksson responded:  2019-09-24

Just some more additional info from me. I was using msconvert (ProteoWizard 3.0.1908 64-bit), but through the TPP distribution. In the Petunia GUI of
TPP, only a handful of msconvert parameters are shown.

When I instead open msconvert as a standalone software, I can see that by default, the titleMaker creates a parameter called NativeID<ID>.


So, could it be that Skyline/Blidbuild is looking for a term 'SpectrumNativeID' that now is replaced by the term 'NativeID'? Then I can understand that
problems could arise.



matt.chambers42 responded:  2019-10-04

Hi Marc,

The spectrumNativeID attribute is expected in the pepXML if the search was MSGF-DB or if the first search_hit element has the spectrumNativeID element. This suggests to me that maybe one of the two search engines included in the iprophet pepXML has the attribute but the other doesn't. If that's not it then I'm not sure what's going on. I'd need to see the file to understand. It's definitely not related to MSConvert: this attribute is only in the pepXML, not the spectrum title (which might be seen in an MGF file).


matt.chambers42 responded:  2019-10-08

I will see about specifically disabling the use of spectrumNativeID when the pepXML source is iprophet.

matt.chambers42 responded:  2019-10-10

This issue should be fixed in the next Skyline-daily or you can try the latest build from:

marc isaksson responded:  2019-10-10

Hi Matt,

thank you very much for fixing this issue. I appreciate it very much!

Best Regards,