Dear Soroush, This option makes use of the TPP's semi-supervised learning mode, which can be used in conjunction with semi-parametric mode, at the user's discretion. Until now, some search engines supported by TPP analysis could only be modeled by PeptideProphet using semi-parametric and semi-supervised that required decoys to be used in the search. Going forward with the new version of the TPP (pre-release version 6.0.0) this is not going to be the case as we will be providing both types of models for more search engine results. I hope this answers your question.
Cheers, -David On Mon, Jan 18, 2021 at 4:02 PM Soroush F <[email protected]> wrote: > Dear all, > > I was wondering when one should use "Use decoy hits to pin down the > negative distribution" in the Peptide Prophet (run through Petunia)? > > If I want to use Target-Decoy approach to estimate FDR in my analysis, > should I use this box, or it has nothing to do with it? > > Thanks, > Soroush > > -- > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/4592e133-201d-4893-9573-ddee56f1071dn%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/4592e133-201d-4893-9573-ddee56f1071dn%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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D-Dc_i9Z393wM_UxV-vFNFLzeLfWdYyA__wFP1i%2BTwQgA%40mail.gmail.com.
