CPFP - The Central Proteomics Facilities Pipeline

CPFP / Cloud CPFP - The Central Proteomics Facilities Pipeline

Core proteomics facilities face difficulties dealing with the analysis of increasing numbers of growing mass-spectrometry datasets. The Central Proteomics Facilities Pipeline (CPFP) has been developed at the University of Oxford and UT Southwesetern Medical Center, based on the tools from the ISB Trans-Proteomic Pipeline. It provides an intuitive web interface for facility staff and clients allowing datasets to be analysed with multiple search engines, their results then combined.

Demo Server Here

Features Include:

Runs on Linux on a single machine, using a local cluster, remote HPC systems, in the AWS cloud, or a combination.
Supports Mascot, X!Tandem, OMSSA search engines and combination of results
Labelled quantitation using ASAPRation, XPRESS, LIBRA from the TPP
Spectral Index Quantation with SINQ
PTM localization scoring with ModLS
Database for all results with quick browsing, comparison between submissions, and easy export to Excel.
Actively developed and used daily in the UTSW and Oxford Proteomics Core Facilities, and open-source under the CDDL license.

Latest News

29th October 2012 - Cloud CPFP Publication

A paper describing and demonstrating CPFP 2.x (Cloud CPFP) has been published in the Journal of Proteome Research:

This paper includes benchmark data showing the performance of CPFP in different configurations using the Amazon cloud and the University of Texas TACC Longhorn 4 HPC cluster.

D. C. Trudgian and H. Mirzaei, Cloud CPFP: A Shotgun Proteomics Data Analysis Pipeline Using Cloud and High Performance Computing J. Proteome. Res, Article ASAP, DOI: 10.1021/pr300694b, 2012. [Journal Link]

21st September 2012 - CPFP 2.0.3 Released

CPFP version 2.0.3 has been released. Key changes for this version include:

ETD support
Reduced size of build
Cloud CPFP fixes
Improved spectrum annotation
ModLS PTM localization improvements

Download CPFP Here

Amazon Web Services AMI IDs Here

Plans for the next releases include:

CPFP 2.1.x will feature a much simplified build process for Linux and OSX users installing from source. In addition, we will begin to provide binary packages for RHEL 6.x and recent Ubuntu Linux distributions. A Scientific Linux based VMWare image will be offered for users wishing to try out the software locally as a virtual machine.

CPFP 2.2.x will feature screen-by-screen help, and various user interface improvements. The TPP version used by CPFP will be updated, and the installation process will be further refined.

Contact Details

If you have questions about CPFP please contact David Trudgian via email at david.trudgian@utsouthwestern.edu.

Note that support is limited - advice will be given as time permits.

Availability

CPFP has been released freely under the open source CDDL license, and can be downloaded here. Direct access to the development git source repository is available.

A demonstration server with guest access is provided by UTSW.

For further details of the features of CPFP take a look at the overview. Tutorial, installation, and administration documentation can be found using the links on the side bar to the right.

Publications & Acknowledgments

If you use CPFP for published work please cite the following reference:

D. C. Trudgian, B. Thomas, S. J. McGowan, B. M. Kessler, M. Salek and O. Acuto, CPFP: a central proteomics facilities pipeline, Bioinformatics, 26(8), pp. 1131-1132, 2010. [Journal Link]

For Cloud CPFP (version 2.x and above):

D. C. Trudgian and H. Mirzaei, Cloud CPFP: A Shotgun Proteomics Data Analysis Pipeline Using Cloud and High Performance Computing J. Proteome. Res, Article ASAP, DOI: 10.1021/pr300694b, 2012. [Journal Link]

If you use the SINQ label-free quantitation functionality please cite:

D. C. Trudgian, G. Ridlova, R. Fischer, M. M. Mackeen, N. Ternette, O. Acuto, B. M. Kessler and B. Thomas, Comparative evaluation of label-free SINQ normalized spectral index quantitation in the central proteomics facilities pipeline. PROTEOMICS, 11 (14), pp. 2790-2797, 2011. [Journal Link]

CPFP has been built on tools from the ISB TPP, and includes / uses software from the NCBI and EBI. We are grateful to the authors of all software used by CPFP for their efforts in developing this software, and distributing their work freely.

We wish to acknowledge the Computational Biology Research Group, Medical Sciences Division, Oxford for use of their services in this project. We wish to thank OSSWatch and Matthew Loryman (University of Oxford Research Services) for aiding the release of this software.

Full funding information and other acknowledgements may be found on the acknowledgements page of this site.