Endogenous peptide identification

[sudarshan kumar]

Dear members, 

I am new to this group. Can anyone help me get a standard refined search parameters either in comet or tandem or in any other search engine  to identify endogenous peptides.

1. These peptides have not been cleaved by any enzyme

2. Modification are typically not as those which happen during trypsin digestion. 

3. Is FDR <1% in decoy search good in this case?

Please reply if you have any clues. 

Reg,

sud 

[Eric Deutsch]

Hi Sud, I think you can just use this parameter with Comet:

 

search_enzyme_number = 0               # choose from list at end of this params file

 

where 0 is defined at the bottom of the comet.params:

 

[COMET_ENZYME_INFO]

0.  Cut_everywhere         0      -           -

1.  Trypsin                1      KR          P

 

This tends to be a very computationally expensive search, so limiting your sequence database to a modest size would be beneficial.

 

Eric

--
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-discu...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/2789dfd2-297a-4981-8233-70c799f96e77n%40googlegroups.com.

[sudarshan kumar]

Thank you so much Eric, 

I will  use this....  

Regards 

To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/4212a4c3ac6dc5118bbcc77f62ba4b56%40mail.gmail.com.