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.
