MS Amanda search result files? dkueltz  2020-10-12
 

Hi Nick,
Are the msamanda search results stored somewhere in a format that can be imported into Scaffold or other viewers? It would be useful to have those search result files for comparison with other search engines.
Thanks,
Dietmar

 
 
matt.chambers42 responded:  2020-10-12

Hi Dietmar,

Do you see the .mzid and .mzid.gz files created alongside your input files?

 
dkueltz responded:  2020-10-13

Hi Matt,
Yes, I saw those files butScaffold, PeptideShaker, etc they seem to require a corresponding mgf file with the mzid file. I was not able to load just the mzid into either Scaffold nor Peptideshaker.
Dietmar

 
matt.chambers42 responded:  2020-10-13

The RAW/WIFF/mzML file is what you'd use to provide the spectra to go with the identifications, although those really shouldn't be absolutely necessary to view and analyze identifications: that's an unfortunate restriction of those programs (presumably to ensure you can view the annotated spectra). If those programs don't accept the vendor format (I think Scaffold does but PeptideShaker is unfortunately stuck on MGF) you may have to convert them to an open format. Converting to MGF but having done the search on the vendor files is not likely to work with PeptideShaker though. Likely you'd have to search the MGF files rather than the vendor files. But I'm not sure Skyline's peptide search is currently configured to work like that because MGF can't have the MS1s, and Skyline will currently assume you want to do MS1 quant after building the library. It's really too bad that PeptideShaker only supports MGF because it's otherwise quite nice. https://github.com/compomics/peptide-shaker/issues/140