Hi Mike, Thanks a lot. I am able to use percolator now in TPP. I have one more query regarding Kojak - If I am not wrong, PeptideProphet can work even without Decoy using the learned model of correct and incorrect assignment. Does it work for search results of Kojak as well. I tried both (with and without Decoy) ways and I got completely different results. I could run both of them successfully. However, in case of "without Decoy" I am getting around 2,500 cross linked peptides at 1% FDR. In the other case (with Decoy), I am getting hardly 15-20 peptides.
Please suggest the needful. Thanks & Regards -Kamal On Thu, Sep 27, 2018 at 2:28 PM Michael Hoopmann < [email protected]> wrote: > 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:* [email protected] [mailto: > [email protected]] *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 [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. > > -- > You received this message because you are subscribed to a topic in the > Google Groups "spctools-discuss" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/spctools-discuss/DOWTSTHZv44/unsubscribe > . > To unsubscribe from this group and all its topics, 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. > -- Kamal Mandal, M.Tech Research Scholar National Institute of Immunology, New Delhi Aruna Asaf Ali Marg New Delhi - 110067 *India* *Contact no. :- +91- 9560445356 * -- 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.
