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NAME
CPFP - The Central Proteomics Facilities Pipeline
DESCRIPTION
CPFP provides a comprehensive MS/MS shotgun-proteomics data analysis
pipeline, based on tools from the Trans Proteomic Pipeline (TPP), which
was initially developed at the Institute of Systems Biology (Seattle).
The TPP is a commonly adopted data analysis pipeline, but has a limited
web interface.
CPFP is designed for the needs of proteomics core facilities. Therefore
it provides an intuitive web interface for users, and facilitates
dissemination of data from facility staff to facility clients. All
data-set submissions, searches, and results are stored in a database.
This allows quick and easy access to results via web viewers, and export
into Excel format etc. The results database also allows users to search
across all of their submissions for peptides or proteins in a single
step, rather than having to interrogate each search results separately.
CPFP currently supports searches with Mascot, X!Tandem, Comet,
Myrimatch, MS-GF+ and OMSSA. Search results are validated and combined
using the PeptideProphet, InterProphet, and ProteinProphet tools from
the TPP. LIBRA from the TPP is used for iTRAQ quantitation. XPRESS and
ASAPRatio from the TPP are used for isotope-labelled quantitation.
Additional tools developed for the TPP include SINQ, which performs
label-free quantitation using the spectral index method, and ModLS,
which performs post-translational modification (PTM) localization
scoring.
CPFP can be installed in various configurations. It can run on a single
machine, or can make use of local or remote GridEngine clusters, or the
Amazon AWS cloud.
See the INSTALL file for installation details.
LICENSE
This software is licensed under the CDDL, and incorporates third-party
software under compatible licenses.
Please see the LICENSE, LICENSE_CDDL and THIRD_PARTY_LICENSES files for
full information.
WEBSITE
The website for CPFP is located at:
http://cpfp.sourceforge.net
The site contains a demo installation, release downloads, the
development source code repositories, documentation and further
information.
REFERENCES
CPFP was described in:
D C Trudgian et al. CPFP: a central proteomics facilities pipeline.
Bioinformatics 26(8), pp 1131-1132, 2010
http://bioinformatics.oxfordjournals.org/cgi/content/short/26/8/1131
Please cite this paper if you use CPFP in published work.
SINQ, the CPFP tool for spectral index quantitation was described in:
D. C. Trudgian et al. Comparative Evaluation of Label-Free SINQ
Normalized Spectral Index Quantitation in the Central Proteomics
Facilities Pipeline, PROTEOMICS, Accepted Publications doi:
10.1002/pmic.201000800, 2001
http://onlinelibrary.wiley.com/doi/10.1002/pmic.201000800/abstract
Please cite this paper if you use SINQ in published work.
ACKNOWLEDGMENTS
Software
CPFP is based on tools from the ISB Trans-Proteomic Pipeline (TPP) which
originated at the Institute of Systems Biology (Seattle), and now has
many contributors from around the globe. For information see the
SPCtools Wiki:
http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP
CPFP includes X!Tandem,an open-source mass-spectrometry search engine
available from the Global Proteome Organization:
http://www.thegpm.org/TANDEM/index.html
CPFP includes OMSSA is an open-source mass-spectrometry search engine
available from the NCBI: http://pubchem.ncbi.nlm.nih.gov/omssa/
Details of other 3rd party software included in the CPFP can be found in
the 3rd party licenses file: THIRD_PARTY_LICENSES
Contributions
Initial development of CPFP was performed by Dr. David Trudgian at the
University of Oxford. This development took place within the Oxford
Central Proteomics Facilities, Computational Biology Research Group, and
Ratcliffe / Pugh laboratory.
From September 2011 development on CPFP has been led by Dr. David
Trudgian in the Mirzaei Laboratory / Proteomics Core, Department of
Biochemistry, UT Southwestern Medical Center, Dallas TX. Development
also continues at the University of Oxford, within the Central
Proteomics Facilities.
The developers wish to acknowledge the academic, funding, and
computational contributions of the following persons who have aided the
development and maintenance of CPFP:
University of Oxford
Dr. B. Thomas, Dr. B. M. Kessler, Prof. O. Acuto, Dr. S. McGowan,
Prof. P. J. Ratcliffe, Dr. H. Kramer, Dr. N. Ternette, Dr. R.
Fischer, Dr. C. Casals-Pascual, Mr. S. Taylor, Dr. Z-P. Han, Ms. G.
Ridlova, Mr. S. Loreyman, OSSWatch.
UT Southwestern Medical Center
Dr. H. Mirzaei, Dr. X. Guo.
Funding
Funding contributing to the development of this software has been
provided by various sources, including:
* John Fell OUP Research Award to Dr. B. M. Kessler (University of
Oxford).
* The EPA Trust to the Sir William Dunn School of Pathology Central
Proteomics Facility (University of Oxford).
* ERC FP7 Grant (project 233240) to Professors P. J. Ratcliffe and C.
J. Schofield (University of Oxford).
* Cancer Prevention & Research Institute of Texas (CPRIT) grants
RP120613 and R1121 to Dr. H. Mirzaei (UT Southwestern Medical
Center).
AUTHOR
Created By: D. C. Trudgian, University of Oxford.
Modified By: D. C. Trudgian, University of Texas Southwestern Medical
Center.
Phil Charles
Aishwarya Sundaresan
