Hello Jesse, As you noted, the CLEVEL used in your analysis is set to 5. This means that any PSM with an f-val not higher than 5 standard deviations from the estimated mean f-value of the false PSMs, will automatically be forced to a probability of 0 during modeling. This excludes all the high scoring DECOYS from further analysis since they are given a probability of 0. I would suggest you lower your CLEVEL value to achieve more PSMs with lower f-values but probabilities greater than 0 after PeptideProphet. It appears that the software is working as designed in this case. Normally you should set your CLEVEL as low as possible to give decent modeling without throwing away too many good PSMs. You should be able to get decent results with a much smaller CLEVEL on this dataset 0, 0.5 should all work well here, see attached. Also you can boost the correct peptide IDs if you enable the iProphet modeling and analysis on this data.
Cheers, -David On Mon, Jun 27, 2016 at 3:52 PM, Jesse <[email protected]> wrote: > Also here are links to the pepxml files before and after peptide prophet: > > > https://drive.google.com/file/d/0B4N83JlasjgsemxITVZUNGpWdVk/view?usp=sharing > > > https://drive.google.com/file/d/0B4N83JlasjgsUE9iRmNEZU5zSEk/view?usp=sharing > > > On Monday, June 27, 2016 at 12:27:50 PM UTC-7, Jesse wrote: >> >> Hello TPP team, >> >> I've running some files through PeptideProphet using the xinteract >> interface, and I think I'm not getting enough decoy hits resulting in way >> too many correct IDs reported (evidenced by manual spectra review of >> hits). Please see the attached model results where no setting of min. >> Probability results in a 1% FDR and causes all results to be accepted. >> >> I think this is somehow related to the c-level parameter? I tried >> setting it even higher and that does decrease the IDs but there is always >> the same number of true hits (second attached screenshot). >> >> Otherwise, maybe I need to search my data with looser tolerances to get >> more decoy hits? >> >> Your help is appreciated. >> >> Best regards, >> Jesse >> > -- > 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 post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- 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 post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
