Central Proteomics Facilities Pipeline
f52e8676 — Phil Charles 4 years ago
Merge branch 'oxford'
50c48673 — Phil Charles 4 years ago
Fixes to LDAP username lookup to handle large number of LDAP users (add paging, support for authenticated bind)
076d3635 — Phil Charles 4 years ago
Add some handling for edge-case scenarios where compressed fragment spectrum JSON data is larger than 65kb (and try to prevent this scenario, which can happen with profile MSMS spectra without a Top200 filter).  This was causing unexplained failure of SINQ Tasks.

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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.