spectral library from Peaks Online pepXML

spectral library from Peaks Online pepXML Tharan Srikumar  2020-11-11

Hi Skyline team,

I'm trying to use exports from Peaks Online v1.4 to create a spectral library in Skyline daily (yesterday's release). I've exported pepXML, MzIdenML and a mgf. If I rename the pepXML file from the original .xml to pepXML, Skyline begins to read the file, but throws an error looking for the spectra file. It seems like Skyline is not looking for the mgf file but rather several other formats (see screenshot attached). I've also tried to rename the mgf file to the same filename Skyline is requesting with no success either.



matt.chambers42 responded:  2020-11-11

Hi Tharan,

Can you export a different spectrum format from PEAKS? Either mzML or mzXML will work. It is often tricky to match spectra between pepXML and MGF, although I haven't seen that particular file combination before from PEAKS.

Hope this helps,

Tharan Srikumar responded:  2020-11-11

Hi Matt,

mgf seems to be the only option in Peaks Online. I'll double check with the BSI team. Would it help if I share the pepXML file and mgf?



matt.chambers42 responded:  2020-11-12

Yes, that would help.

Tharan Srikumar responded:  2020-11-12