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

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.accessioned2017-08-17T21:48:23Z
dc.date.available2017-08-17T21:48:23Z
dc.date.issued2009-05-27
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.grantingagencyNatural Sciences and Engineering Research Council (NSERC) of Canada, the Canada Research Chair program and the Alberta Heritage Foundation for Medical Research (AHFMR)en_US
dc.description.refereedYesen_US
dc.description.sponsorshipFinancial support for this study was provided by grants from the Natural Sciences and Engineering Research Council (NSERC) of Canada. DCS gratefully acknowledges the support of the Canada Research Chair program and the Alberta Heritage Foundation for Medical Research (AHFMR).en_US
dc.identifier.citationSlysz, G. W., Baker, C. A., Bozsa, B. M., Dang, A., Percy, A. J., Bennett, M., & Schriemer, D. C. (2009). Hydra: software for tailored processing of H/D exchange data from MS or tandem MS analyses. BMC Bioinformatics, 10, 162. http://doi.org/10.1186/1471-2105-10-162en_US
dc.identifier.doi10.1186/1471-2105-10-162
dc.identifier.doihttp://dx.doi.org/10.11575/PRISM/33795
dc.identifier.urihttp://hdl.handle.net/1880/52195
dc.language.isoenen_US
dc.publisherBMC Bioinformaticsen_US
dc.publisher.departmentBiochemistry and Molecular Biologyen_US
dc.publisher.facultyFaculty of Medicineen_US
dc.publisher.institutionUniversity of Calgaryen_US
dc.publisher.urlhttps://bmcbioinformatics.biomedcentral.comen_US
dc.subjectHydrogen/deuteriumen_US
dc.subjectmass spectrometryen_US
dc.titleHydra: software for tailored processing of H/D exchange data from MS or tandem MS analysesen_US
dc.typejournal article
Files
Original bundle
Now showing 1 - 1 of 1
Loading...
Thumbnail Image
Name:
1471-2105-10-162.pdf
Size:
2.42 MB
Format:
Adobe Portable Document Format
Description:
Main Article
License bundle
Now showing 1 - 1 of 1
Loading...
Thumbnail Image
Name:
license.txt
Size:
1.95 KB
Format:
Item-specific license agreed upon to submission
Description: