title: Hydra: software for tailored processing of H/D exchange data from MS or tandem MS analyses.
abstract: BACKGROUND
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, T2N 4N1, Canada. gslysz@ucalgary.ca
authors.forename: Gordon W
authors.initials: GW
authors.lastname: Slysz
authors.forename: Charles A H
authors.initials: CA
authors.lastname: Baker
authors.forename: Benjamin M
authors.initials: BM
authors.lastname: Bozsa
authors.forename: Anthony
authors.initials: A
authors.lastname: Dang
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Percy
authors.forename: Melissa
authors.initials: M
authors.lastname: Bennett
authors.forename: David C
authors.initials: DC
authors.lastname: Schriemer
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D030562:Databases, Protein; D041961:Deuterium Exchange Measurement; D013058:Mass Spectrometry; D015233:Models, Statistical; D010446:Peptide Fragments / Q000737:chemistry; D010455:Peptides / Q000737:chemistry; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D012984:Software; D053719:Tandem Mass Spectrometry; D014584:User-Computer Interface
chemical_list: D010446:Peptide Fragments; D010455:Peptides; D011506:Proteins