In the ideal case where the PeptideProphet and iProphet had perfect discriminating power, i.e. the correct and incorrect PSM distributions do not overlap, you would expect a large peak at P=0 and P=1 and nothing in between. As a dataset diverges from this ideal and the correct and incorrect distributions begin to overlap, you will still have very large peaks near P=0 and near P=1, with a small number of intermediate values where the probability is between 0 and 1.
So, in short, your distribution is exactly what you would expect based on what you did. It is indicative of a great dataset. You should follow David’s suggestion, and then if you replot, you will see huge peaks at 0 and 1 with rather little in between. Regards, Eric *From:* [email protected] [mailto: [email protected]] *On Behalf Of *David Shteynberg *Sent:* Tuesday, January 03, 2017 10:36 AM *To:* spctools-discuss *Subject:* Re: [spctools-discuss] PeptideProphet/iProphet Probability Distribution 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. -- 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.
