Hi Phil, I have a 15 hek files searched with Mascot, X!Tandem and MSGF+ separately. I am trying to create a library using TPP pipeline and SpectraST. I have convert the results individually to pepxml using Mascot2XML, Tandem2XML and Idconvert and then apply peptideprophet on each file. My question is about the next step, Should I be merging individual search engine results using iprophet and to make three combined files and then merge them again using iprophet? Or I merge each run from three searches together using iprophet and then merge the resulting 15 files together to apply ProteinProphet or Mayu ?
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