Hi Srikanth, I suggest after your step “I have convert the results individually to pepxml using Mascot2XML, Tandem2XML and Idconvert and then apply peptideprophet on each file” (which is good), the next step is merge the 3 PeptideProphet outputs into a single PepXML file with iProphet. Then build your spectral library from that one file.
Regards, Eric *From:* spctools-discuss@googlegroups.com <spctools-discuss@googlegroups.com> *On Behalf Of *Srinivas Srikanth *Sent:* Monday, June 8, 2020 9:43 PM *To:* spctools-discuss <spctools-discuss@googlegroups.com> *Subject:* [spctools-discuss] Spectral library generation 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 ? Srikanth -- 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 spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/08ebe555-a53b-4c20-8ac8-14709b4f2d49o%40googlegroups.com <https://groups.google.com/d/msgid/spctools-discuss/08ebe555-a53b-4c20-8ac8-14709b4f2d49o%40googlegroups.com?utm_medium=email&utm_source=footer> . -- 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 spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/576844661964d7ee08689ef8a2002609%40mail.gmail.com.
