Hi Kamal, Yes, you can use PeptideProphet to validate Kojak results. Select “Kojak” from your pipeline in the upper right of the TPP page, and it will default PeptideProphet parameters for Kojak. Input is the PepXML output from Kojak.
The windows version of Percolator can be found here: https://github.com/percolator/percolator/releases To use it in the TPP do the following: 1. Install Percolator on your computer. 2. Go into the Percolator bin folder (usually something like C:\Program Files\Percolator\bin\) and copy percolator.exe 3. Paste it into your TPP bin folder (usually something like C:\TPP\bin\) 4. In the TPP, select “External Tools->Percolator” from the menu. Input is the .perc.txt output files from Kojak. Cheers, Mike From: spctools-discuss@googlegroups.com [mailto:spctools-discuss@googlegroups.com] On Behalf Of Kamal Mandal Sent: Thursday, September 27, 2018 12:17 PM To: spctools-discuss Subject: [spctools-discuss] Kojak Hello, Is it possible to use PeptideProphet for validation of data (Cross-linked peptides) obtained from Kojak search in TPP. Is the windows version of percolator available and how do we integrate that to TPP suite? Thanks, -Kamal -- 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 post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout. -- 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 post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
