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Protocols

FDRAnalysis specifications

Information


Unique identifier OMICS_17462
Name FDRAnalysis
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Simon Hubbard

Publication for FDRAnalysis

FDRAnalysis citations

 (3)
call_split

Using the entrapment sequence method as a standard to evaluate key steps of proteomics data analysis process

2017
BMC Genomics
PMCID: 5374549
PMID: 28361671
DOI: 10.1186/s12864-017-3491-2
call_split See protocol

[…] Four commonly used quality control methods were used in this study, including BuildSummary [], PeptideProphet [–], FDRAnalysis [] and PepDistiller [], all of which produced a rescore of Mascot results for each PSM: BuildSummary’s ExpectValue, PeptideProphet’s probability, FDRAnalysis’s FDRScore and PepDistiller’s […]

library_books

Scientific workflow optimization for improved peptide and protein identification

2015
BMC Bioinformatics
PMCID: 4558836
PMID: 26335531
DOI: 10.1186/s12859-015-0714-x

[…] have also published efforts in combining multiple algorithms for peptide-spectrum matching, for instance the framework developed by Searle et al. [], the MSblender software from Kwon et al. [] or the FDRAnalysis algorithm of Wedge et al. []. Recently, in de Bruin et al. [] and Mohammed et al. [] we have shown how some of these algorithms can be integrated with other algorithms in scientific workfl […]

library_books

Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective☆

2014
Biochim Biophys Acta
PMCID: 3898926
PMID: 23467006
DOI: 10.1016/j.bbapap.2013.02.032

[…] de.com) is a Java library which enables the upload of peptide identification results from target/decoy searches carried out by three different search engines: Mascot, OMSSA and X!Tandem. Importantly, FDRAnalysis can import native format search results, and supports mzIdentML.Several other algorithms and libraries have been developed to solve the protein inference problem . IDPicker (http://fenchu […]

Citations

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FDRAnalysis institution(s)
Faculty of Life Sciences, University of Manchester, UK; Institute of Integrative Biology, University of Liverpool, Liverpool, UK
FDRAnalysis funding source(s)
This work was supported by the Institute of Integrative Biology, University of Liverpool [BBSRC: BB/G010781/1] and the Faculty of Life Sciences, University of Manchester [BBSRC: BB/F004605/1].

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