Anyone try something simliar to the described protocol? We took all our RAW files and converted them to OUT files using bioworks seqeust search. Then using TPP software, we converted all OUTfiles (with a params file) to pepXML. However, using peptide prophet required doing it in groupsfor it to work properly, so we decided we'll just make a few libraries as opposed to one so we can select all of them in skyline (our final objective).
However, when building a skyline library using command prompt, it seems to be looking for the mzXML files as well as the pepXML files, although we never started with mzXML files beceause we just converted RAW files to pepXML. Would making new mzXML files from the RAW files fix this problem? Wouldn't all the relevant information be located in the peptide prophet output pepXML? Thanks, Sayeef Moffitt proteomics -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
