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Citations per year

Number of citations per year for the bioinformatics software tool CPFP
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Tool usage distribution map

This map represents all the scientific publications referring to CPFP per scientific context
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Protocols

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 citations

 (24)
library_books

Dysregulation of fibulin 5 and matrix metalloproteases in epithelial ovarian cancer

2018
Oncotarget
PMCID: 5865667
PMID: 29581841
DOI: 10.18632/oncotarget.24484

[…] sociation (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) [] against the appropriate […]

library_books

Snapin promotes HIV‐1 transmission from dendritic cells by dampening TLR8 signaling

2017
PMCID: 5641917
PMID: 28923824
DOI: 10.15252/embj.201695364

[…] uce 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, ), to […]

library_books

Pet10p is a yeast perilipin that stabilizes lipid droplets and promotes their assembly

2017
PMCID: 5626530
PMID: 28801319
DOI: 10.1083/jcb.201610013

[…] higher-energy 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 against the S. […]

library_books

Type VI secretion system MIX‐effectors carry both antibacterial and anti‐eukaryotic activities

2017
EMBO Rep
PMCID: 5666596
PMID: 28912123
DOI: 10.15252/embr.201744226

[…] ectrometer 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 […]

call_split

A novel workflow combining plaque imaging, plaque and plasma proteomics identifies biomarkers of human coronary atherosclerotic plaque disruption

2017
PMCID: 5477097
PMID: 28642677
DOI: 10.1186/s12014-017-9157-x
call_split See protocol

[…] ery 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, OMSS […]

library_books

Phosphorylation of iRhom2 at the plasma membrane controls mammalian TACE dependent inflammatory and growth factor signalling

2017
eLife
PMCID: 5436907
PMID: 28432785
DOI: 10.7554/eLife.23968.016

[…] ected into the Ultimate 3000 RSLCnano HPLC (Dionex) – tandem mass spectrometry Q Exactive Orbitrap machine. Data was analysed using the semi-quantitative label-free quantitation method SINQ () of the central proteomics facilities pipeline (CPFP) Oxford (; ). Phosphopeptides were identified and analysed with the MASCOT software. […]


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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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