Thank you so much Eric, I will use this.... Regards On Fri, Dec 11, 2020, 05:06 'Eric Deutsch' via spctools-discuss < spctools-discuss@googlegroups.com> wrote:
> 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 > > > > > > > > *From:* spctools-discuss@googlegroups.com < > spctools-discuss@googlegroups.com> *On Behalf Of *sudarshan kumar > *Sent:* Thursday, December 10, 2020 2:11 AM > *To:* spctools-discuss <spctools-discuss@googlegroups.com> > *Subject:* [spctools-discuss] Endogenous peptide identification > > > > 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 > > > > > > -- > 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/2789dfd2-297a-4981-8233-70c799f96e77n%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/2789dfd2-297a-4981-8233-70c799f96e77n%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/4212a4c3ac6dc5118bbcc77f62ba4b56%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/4212a4c3ac6dc5118bbcc77f62ba4b56%40mail.gmail.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/CALZrgHS36KD2i%2BRF3vZTEoZoL_%3DEDvfSKenxgAZ%3D_XUj0v0eqg%40mail.gmail.com.
