Hydra: software for tailored processing of H/D exchange data from MS or tandem MS analyses

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dc.contributor.authorSlysz, Gordon W.
dc.contributor.authorBaker, Charles A. H.
dc.contributor.authorBozsa, Benjamin M.
dc.contributor.authorDang, Anthony
dc.contributor.authorPercy, Andrew J.
dc.contributor.authorBennett, Melissa
dc.contributor.authorSchriemer, David C.
dc.date.accessioned2009-06-22T20:53:52Z
dc.date.available2009-06-22T20:53:52Z
dc.date.issued2009-5-27
dc.description.abstractBackground Hydrogen/deuterium exchange mass spectrometry (H/DX-MS) experiments implemented to characterize protein interaction and protein folding generate large quantities of data. Organizing, processing and visualizing data requires an automated solution, particularly when accommodating new tandem mass spectrometry modes for H/DX measurement. We sought to develop software that offers flexibility in defining workflows so as to support exploratory treatments of H/DX-MS data, with a particular focus on the analysis of very large protein systems and the mining of tandem mass spectrometry data. Results We present a software package ("Hydra") that supports both traditional and exploratory treatments of H/DX-MS data. Hydra's software architecture tolerates flexible data analysis procedures by allowing the addition of new algorithms without significant change to the underlying code base. Convenient user interfaces ease the organization of raw data files and input of peptide data. After executing a user-defined workflow, extracted deuterium incorporation values can be visualized in tabular and graphical formats. Hydra also automates the extraction and visualization of deuterium distribution values. Manual validation and assessment of results is aided by an interface that aligns extracted ion chromatograms and mass spectra, while providing a means of rapidly reprocessing the data following manual adjustment. A unique feature of Hydra is the automated processing of tandem mass spectrometry data, demonstrated on a large test data set in which 40,000 deuterium incorporation values were extracted from replicate analysis of approximately 1000 fragment ions in one hour using a typical PC. Conclusion The customizable workflows and user-friendly interfaces of Hydra removes a significant bottleneck in processing and visualizing H/DX-MS data and helps the researcher spend more time executing new experiments and interpreting results. This increased efficiency will encourage the analysis of larger protein systems. The ability to accommodate the tandem MS dimension supports alternative data collection and analysis strategies, as well as higher resolution localization of deuteration where permitted by the fragmentation mechanism.en_US
dc.description.refereedYes
dc.description.sponsorshipFunding provided by the Open Access Authors Fund.en_US
dc.identifier.citationSlysz GW, Baker CAH, Bozsa BM, Dang A, Percy AJ, Bennett M, Schriemer DC "Hydra: software for tailored processing of H/D exchange data from MS or tandem MS analyses". BMC Bioinformatics 2009, 10:162 (27 May 2009)en_US
dc.identifier.doi10.1186/1471-2105-10-162
dc.identifier.doihttp://dx.doi.org/10.11575/PRISM/33792
dc.identifier.issn1471-2105en_US
dc.identifier.urihttp://hdl.handle.net/1880/47342
dc.language.isoenen_US
dc.publisherBMC Bioinformatics
dc.publisher.departmentBiochemistry and Moleculary Biology
dc.publisher.facultyMedicine
dc.publisher.institutionUniversity of Calgaryen_US
dc.publisher.urlhttp://www.biomedcentral.com/en_US
dc.titleHydra: software for tailored processing of H/D exchange data from MS or tandem MS analyses
dc.typejournal article
thesis.degree.disciplineBiochemistryeng
thesis.degree.disciplineOncology
thesis.degree.disciplinePharmacology
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