Hi All, I am analyzing the SWATH-MS data using the DIA-Umpire. And I have 3 data files of same sample which lead to generation of 9 .mgf output files from DIA-Umpire, which were converted into 9 mzXML and then subjected to Comet and X! Tandem search, and subsequently to peptide prophet and hence total files generated during this process are 18 pep.xml files. My ultimate aim to build the assay library. So, I am confused how to combine the results of these 18 peptideprophet files.
Should I combine the Comet search results of each data file separately and X! Tandem results separately and then combine these outputs again using iProphet? This should result in generation of 3 iprophet result files corresponding to each data file, which can again combined into one file by iProphet in final step? Or there is another way out of this problem? Thanks Ankit -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
