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

Slysz GW, Baker CA, Bozsa BM, Dang A, Percy AJ, Bennett M, Schriemer DC - BMC Bioinformatics (2009)

Bottom Line: Hydra's software architecture tolerates flexible data analysis procedures by allowing the addition of new algorithms without significant change to the underlying code base.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, T2N 4N1, Canada. gslysz@ucalgary.ca

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.

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.

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Related in: MedlinePlus

Deuterium distribution tools. The deuterium distribution can be extracted using the tools in the "DeutDistControl" tab in the "Manual Assessment and Validation" form (see Fig. 7). The distribution is shown as a blue bar graph overlaying the mass spectrum. Parameters for truncating the theoretical and experimental isotopic envelope are controlled by setting the relative threshold (%) or by setting the exact number of peaks to be used in the calculation (see Chik et. al [9]). A truncated isotopic profile can then be 'padded' using the specified number of zero-intensity peaks. The amount of deuteration can be calculated by the weighted average of the reported distribution and this is displayed within the "DeutDistControl" tab.
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Figure 10: Deuterium distribution tools. The deuterium distribution can be extracted using the tools in the "DeutDistControl" tab in the "Manual Assessment and Validation" form (see Fig. 7). The distribution is shown as a blue bar graph overlaying the mass spectrum. Parameters for truncating the theoretical and experimental isotopic envelope are controlled by setting the relative threshold (%) or by setting the exact number of peaks to be used in the calculation (see Chik et. al [9]). A truncated isotopic profile can then be 'padded' using the specified number of zero-intensity peaks. The amount of deuteration can be calculated by the weighted average of the reported distribution and this is displayed within the "DeutDistControl" tab.

Mentions: Multiple algorithms have been described that extract the deuterium distribution of an isotopic profile [6,9,10,16,17], but none of these have been incorporated on a project-wide scale into a convenient user interface to support rapid visualization of deconvolved isotopic distributions. In Hydra, we implement the method described by Chik et al. [9], which uses a linear-least squares approach to fit the deuterium distribution. This can be included as a task within the data processing workflow, and can be further examined in the manual assessment and validation tool, as shown in Fig. 10.


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

Slysz GW, Baker CA, Bozsa BM, Dang A, Percy AJ, Bennett M, Schriemer DC - BMC Bioinformatics (2009)

Deuterium distribution tools. The deuterium distribution can be extracted using the tools in the "DeutDistControl" tab in the "Manual Assessment and Validation" form (see Fig. 7). The distribution is shown as a blue bar graph overlaying the mass spectrum. Parameters for truncating the theoretical and experimental isotopic envelope are controlled by setting the relative threshold (%) or by setting the exact number of peaks to be used in the calculation (see Chik et. al [9]). A truncated isotopic profile can then be 'padded' using the specified number of zero-intensity peaks. The amount of deuteration can be calculated by the weighted average of the reported distribution and this is displayed within the "DeutDistControl" tab.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2696453&req=5

Figure 10: Deuterium distribution tools. The deuterium distribution can be extracted using the tools in the "DeutDistControl" tab in the "Manual Assessment and Validation" form (see Fig. 7). The distribution is shown as a blue bar graph overlaying the mass spectrum. Parameters for truncating the theoretical and experimental isotopic envelope are controlled by setting the relative threshold (%) or by setting the exact number of peaks to be used in the calculation (see Chik et. al [9]). A truncated isotopic profile can then be 'padded' using the specified number of zero-intensity peaks. The amount of deuteration can be calculated by the weighted average of the reported distribution and this is displayed within the "DeutDistControl" tab.
Mentions: Multiple algorithms have been described that extract the deuterium distribution of an isotopic profile [6,9,10,16,17], but none of these have been incorporated on a project-wide scale into a convenient user interface to support rapid visualization of deconvolved isotopic distributions. In Hydra, we implement the method described by Chik et al. [9], which uses a linear-least squares approach to fit the deuterium distribution. This can be included as a task within the data processing workflow, and can be further examined in the manual assessment and validation tool, as shown in Fig. 10.

Bottom Line: Hydra's software architecture tolerates flexible data analysis procedures by allowing the addition of new algorithms without significant change to the underlying code base.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, T2N 4N1, Canada. gslysz@ucalgary.ca

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.

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.

Show MeSH
Related in: MedlinePlus