I have been having a problem with TPP in which ProteinProphet would error out with the response that there are no peptides identified with a probability greater than 0.05, despite the observation that there are many peptides passing the threshold in the pepXML file. This seems to be a common error due to the frequency with which it is discussed. I was able to solve the problem by adding a dbase folder to the working directory and placing the Mascot .fasta file with the sequence database. I also changed the permissions of this folder and the permissions of the working directory using the command line described in the TPP tutorial.
Ex: chmod -R 777 C:\Inetpub\tpp-bin\users\tutorial Once I made these changes the analysis completed smoothly. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
