Dear David,
Thanks so much for your time answering my questions.
I gather from your answer that this option is for TPP. If that is the case,
why does the PeptideProphet probabilities changes when selecting the
option? Am I missing something?
Many thanks.
Soroush
On Tuesday, January 19, 2021
This option changes the way mixture models in the TPP (PeptideProphet) are
generated. The probabilities are estimated based on the mixture models
learned by PeptideProphet. When the mixture models change so will the
probabilities.
On Wed, Jan 20, 2021 at 8:44 PM Soroush F wrote:
> Dear David,
I am not sure I know a tool called "ProptideProphet" ;) Perhaps you tried
to run PeptideProphet but it generated no results for you? When you run
"Analyze Peptides" in the TPP interface, it should create a file called
interact.pep.xml by default, that will contain probabilities among other
Hi David! It works nicely, thank you !
Now I am experiencing another issue of mine :)
I run ProptideProphet on the XML fiel generated by XTandem. I need this
file presuming that PP will add probabilities to the identified peptides as
this is requested by SpectraST to generate the
