Kojak

[Kamal Mandal]

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

[Michael Hoopmann]

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

 

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[Kamal Mandal]

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

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Kamal Mandal, M.Tech

Research Scholar

National Institute of Immunology, New Delhi

Aruna Asaf Ali Marg

New Delhi - 110067

India

 

Contact no. :- +91- 9560445356