I've been using TPP for a little while now for the analysis of my data. I have been using Comet to perform database searching on a large number of mzml files and have noticed that the analysis will usually time out after about 6 hours. In this case, I will remove the mzml files that have been successfully processed and then re-run comet. Is this job time-out an inherent part of TPP, or is it a setting that can be changed? If the latter, are there any risks in running the analysis for over 6 hours?
Thanks in advance for any advice