Central Proteomics Facilities Pipeline (CPFP) is a pipeline for the analysis of MS/MS proteomic data, targeted at the needs of academic proteomics core facilities. The pipeline uses multiple search engines and the Trans Proteomic Pipeline (TPP) tools to provide easy and robust search, validation, and quantitation of LC-MS/MS proteomic datasets.
The CPFP currently supports searches with Mascot (Matrix Science), Tandem (native and k-score), and OMSSA. A single form allows submission to all three programs, without the need to create parameter files and reconcile differences in modification specifications, etc. Processing is performed using jobs on a GridEngine cluster, enabling the pipeline to be scaled up easily as the volume of data to be analysed increases. iTRAQ and isotope labelled quantiation (SILAC / Heavy Dimethyl / iCAT) can be performed within the pipeline.
CPFP was written at the University of Oxford where it is actively developed, and used daily to support the needs of Oxford's core facility. It is released here as open source software under the CDDL licence.