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- person_outline Simon Hubbard
Publication for FDRAnalysis
Using the entrapment sequence method as a standard to evaluate key steps of proteomics data analysis process
[…] 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 […]
Scientific workflow optimization for improved peptide and protein identification
[…] 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 […]
Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective☆
[…] 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 […]
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