Re: [spctools-discuss] Endogenous peptide identification
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. Trypsin1 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 > *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_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_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.
RE: [spctools-discuss] Endogenous peptide identification
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. Trypsin1 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 *On Behalf Of *sudarshan kumar *Sent:* Thursday, December 10, 2020 2:11 AM *To:* spctools-discuss *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_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.
[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.
