|Importing pepXML, mzid, or mzTab from OpenMS in Skyline||lparsons||2019-04-16|
I am attempting to import Peptide Search results into Skyline (188.8.131.5272) that were obtained in OpenMS (in this case using the Comet search engine). The default output from OpenMS is idXML, which is not supported in Skyline. I looked at the options in File -> Import -> Peptide Search and found three possible formats for this though each returned a different error:
pepXML : "file is not from one of the recognized sources"
I checked to make sure these files are reasonable in size; they are all 10-25 MB with 34,000 - 271,000 lines. If I instead continue to work with the idXML file in OpenMS I see plenty of hits as well. If I use the same spectra (in their original raw format) and the same database but instead run it through MaxQuant, I can import the msms.txt file without a problem.
My goal is to import the Peptide Search results and then load a series of MS1-only spectra on top of the results so that peptide quantification can be done using the MS1 spectral data and mapped to the MSMS data of the search results. This works fine if I use the MaxQuant results here instead, though I'm looking to use the Comet (OpenMS) results at this time.