Dear David and Eric Thanks for your replies and suggestions. I thought that I might be able to increase identification by accepting hits with lower thresholds. I do understand what you mentioned here.
Thanks again, Ali On Tuesday, January 3, 2017 at 1:57:38 PM UTC-5, Eric Deutsch wrote: > > 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] <javascript:> [mailto: > [email protected] <javascript:>] *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] <javascript:>> > 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] <javascript:>. > To post to this group, send email to [email protected] > <javascript:>. > 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] <javascript:>. > To post to this group, send email to [email protected] > <javascript:>. > 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.
