CPFP protocols

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CPFP specifications

Information


Unique identifier OMICS_02448
Name CPFP
Alternative name Central Proteomics Facilities Pipeline
Software type Package/Module, Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Perl
Computer skills Advanced
Stability Stable
High performance computing Yes
Maintained Yes

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Publication for Central Proteomics Facilities Pipeline

CPFP in pipeline

2012
PMCID: 3494207
PMID: 22865923
DOI: 10.1074/mcp.M112.020743

[…] using proteowizard msconvert release 3.0.3535 (q exactive data). both tools were used with default parameters except that zlib compression of spectral data was enabled. data was uploaded to the central proteomics facilities pipeline (cpfp at: https://cpfp-master.molbiol.ox.ac.uk/cpfp_demo/auth/login) (). files were searched using mascot version 2.3.01 (matrix science), x!tandem version […]


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CPFP in publications

 (20)
PMCID: 5865667
PMID: 29581841
DOI: 10.18632/oncotarget.24484

[…] (hcd) for ions with charges 2–7. dynamic exclusion was set for 25 s after an ion was selected for fragmentation., raw ms data files were converted to a peak list format and analyzed using the central proteomics facilities pipeline (cpfp), version 2.0.3 [, ]. peptide identification was performed using a non-specific search with the open ms search algorithm (omssa) [] […]

PMCID: 5641917
PMID: 28923824
DOI: 10.15252/embj.201695364

[…] sample complexity and enhance detection of low abundance proteins prior to lc/ms/ms analysis ( and schematic of experimental approach fig b). raw data obtained by lc‐ms/ms was processed using the central proteomics facilities pipeline (cpfp) (trudgian et al, ), which searches three different databases: mascot (matrix science, london, uk), omssa (geer et al, ), and tandem (craig & beavis, […]

PMCID: 5626530
PMID: 28801319
DOI: 10.1083/jcb.201610013

[…] collisional dissociation (hcd) for ions with a charge ≥2. dynamic exclusion was set for 7 s., raw mass spectrometry data files were converted to a peak list format and analyzed using the central proteomics facilities pipeline (cpfp version 2.0.3; ; ). peptide identification was performed using the x!tandem () and open mass spectrometry search algorithm () search engines […]

PMCID: 5666596
PMID: 28912123
DOI: 10.15252/embr.201744226

[…] trometer acquired up to 20 high‐energy, collision‐induced dissociation fragment spectra for each full spectrum acquired., raw ms data files were converted to a peak list format and analyzed using the central proteomics facilities pipeline (cpfp), version 2.0.3 , . peptide identification was performed using the x!tandem and open ms search algorithm (omssa) search engines against the v. proteolyti […]

PMCID: 5477097
PMID: 28642677
DOI: 10.1186/s12014-017-9157-x

[…] rate of 1% and with ion score of >20 were accepted for further analysis. false discovery rate (fdr) of the protein identification was further performed by uploading the converted mgf files to the central proteomics facilities pipeline (cpfp, version 1.3.0 http://www.proteomics.ox.ac.uk/), which combined the searches against the human databases using three different search engines (mascot, […]


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CPFP institution(s)
Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, UK; Henry Wellcome Building for Molecular Physiology, University of Oxford, Roosevelt Drive, Oxford, UK; Computational Biology Research Group, University of Oxford, John Radcliffe Hospital, Oxford, UK
CPFP funding source(s)
Supported by E.P. Abraham Cephalosporin Trust and John Fell OUP Research Fund.

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