Not possible to extract chromatograms from MGF files marc isaksson  2019-10-17


I tried to use Skyline(v.19.1) for MS1 filtering + spectra library building, by importing a mzIdentML file from PeptideShaker (v.1.16.42). While the spectral libraries were built, I got stuck in the peptide search import at the Extract Chromatograms part. The MGF files referred to in the mzIdentML file were missing. SEE ATTACHED.

When I tried to help Skyline locate them by clicking on the Find button, and navigating to the MGF file location, nothing was displayed. Apparently, Skyline does not support the MGF spectra files referred to in the mzIdentML file.

Will MGF files be supported for chromatogram extraction in a later release? Then I could do MS1 filtering on the PeptideShaker result, something which I think would be a nice feature.



Brian Pratt responded:  2019-10-17

Hi Marc,

Do you have the raw data from the mass spec run? That's what Skyline wants to work with for chromatogram extraction.

Thanks for using the Skyline support board,

Brian Pratt

Mike MacCoss responded:  2019-10-17

To follow up, there is no MS1 data in an MGF file. You can use the MGF file to create a spectrum library with the PeptideShaker results but you will then need to give Skyline a file that has MS1 data to perform MS1 filtering. As Brian mentioned, this is most commonly the RAW file itself but it can also be a mzML, mzXML, etc... file. However the RAW file is definitely preferred.


marc isaksson responded:  2019-10-17


I managed to import the search result. It was a little bit confusing since Skyline asked for the missing results file, and showed the paths
to the MGF files used for the database searches.

But after adding the RAW files instead, everything worked out.

Once again, thank you!