Novor, although not bundled with TPP for licensing reasons, is a very fast and capable de novo sequence search engine. If Novor is installed on the machine running TPP, it can be executed via the TPP interface, its output converted to pepXML, and then integrated with downstream TPP tools. Since the scores are not very amenable to modeling, and there is no target-decoy approach to guide the models, an effective approach is to create a sequence database from the Novor output, and then run Comet or another search engine with the new sequences included in the sequence FASTA file, and then let the search engine-score modeling provide downstream probability values and FDR control.