Hi David, sorry for the mistypos!
Yes I run PeptideProphet under Analyze Peptides, and no relevant messages were generated :)
However, I forgot to mention that the problem is related to interact.pep.xml processing in SpectraST in its command line version (independent from TPP).
I am sorry, I did not notice that TPP includes an option for spectral library generation that works perfectly fine, and this is what I needed..!
Just last question, is there any tool for visualisation/inpection of spectra in splib libraries ?
Lots of thanks,