These results are showing you that iProphet has great discriminating power even when you restrict the input to only non-low probability PSMs (filtering with PeptideProphet probability). The best way to run iProphet is to give it all the data from PeptideProphet (use a PeptideProphet minimum probability of 0).
-David On Mon, Jan 2, 2017 at 9:26 PM, Ali <[email protected]> wrote: > Dear all > > > I am plotting the distribution of the assigned PeptideProphet and iProphet > probabilities to my search results. I am seeing a rather strange pattern > shown below. Why am I seeing so many hits with very high confidence > (probability >0.98) but suddenly after that threshold the number of > assigned probabilities to the PSMs decrease abruptly? What could be the > reason for this pattern? One would expect to see all ranges of > probabilities for PSMs. > > > <https://lh3.googleusercontent.com/-BeikGpozjkw/WGsygFV83UI/AAAAAAAABAg/DcG6lRxucM4IRclvdadal-eFSaA05sd6QCLcB/s1600/Picture1.png> > > > This figure is the combination of different search engines: > - Comet (min PepPro=0.5) > - X! Tandem GPM (min PepPro=0.05) > - X! Tandem TPP (min PepPro=0.05) > > The horizontal axis is between 0.5 and 1. > > and I can see the same pattern for the PeptideProphet distribution of each > one of these search engine results including SpectraST (Except for X! > Tandem GPM). > > Thank you very much, > > Ali > > > -- > 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.
