Hi Niko,
Thanks for your question and interest in the TPP.
The PepXMLViewer.cgi tool can be used to display, filter and export pepXML
data, including PTMProphet processed results. PTMProphet computes several
statistics for each PSM and for each PTM analyzed:
Mean Best Probability -- is the aver
Hi,
thanks for all the effort you put into TPP and PTMProphet.
We are currently analyzing some datasets of synthetic phosphopeptides with
PTMProphet and wondered where to set the cut-off for the best localization
score. A score above 0.750 was often used in literature and we tend to use
a sim
