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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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Manual assessment and validation in Hydra. The 'Manual assessment and validation' tool allows inspection and adjustment of individual experiments. Shown here is the replicate viewing mode, selected in the top left. XIC's and MS spectra from replicates are vertically aligned, to aid detection of anomalies. In this example, a particular peptide is selected from the project tree on the left. The XICs (left-most graphs) are very similar, while the second MS spectrum is different from the others. The user can then adjust the XIC selection (peak selection, XIC integration width or offset) using the controls in the right-most panel. The file will automatically reprocess as defined in the workflow. The right-most area also contains controls for displaying deuterium distributions, and extracting raw values (see lower-right hand portion of the figure).
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Figure 8: Manual assessment and validation in Hydra. The 'Manual assessment and validation' tool allows inspection and adjustment of individual experiments. Shown here is the replicate viewing mode, selected in the top left. XIC's and MS spectra from replicates are vertically aligned, to aid detection of anomalies. In this example, a particular peptide is selected from the project tree on the left. The XICs (left-most graphs) are very similar, while the second MS spectrum is different from the others. The user can then adjust the XIC selection (peak selection, XIC integration width or offset) using the controls in the right-most panel. The file will automatically reprocess as defined in the workflow. The right-most area also contains controls for displaying deuterium distributions, and extracting raw values (see lower-right hand portion of the figure).

Mentions: Hydra also provides a means for 'drilling down' to allow visual assessment, manual validation and reprocessing of individual replicates. Fig. 8 shows a screenshot of the 'Manual Assessment and Validation' form, whose arrangement resembles that of Hydra's main display: the left-side for navigation, the center for XIC and MS graphs. The right-side contains controls for adjusting the individual replicates (see below). There are three viewing modes: 'quick view' for viewing single replicates; 'replicate view' for vertically displaying all replicates of a given protein state/labeling condition/peptide/fragment (as shown in Fig. 8); and 'Protein state compare view' for vertically comparing data across protein states.


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)

Manual assessment and validation in Hydra. The 'Manual assessment and validation' tool allows inspection and adjustment of individual experiments. Shown here is the replicate viewing mode, selected in the top left. XIC's and MS spectra from replicates are vertically aligned, to aid detection of anomalies. In this example, a particular peptide is selected from the project tree on the left. The XICs (left-most graphs) are very similar, while the second MS spectrum is different from the others. The user can then adjust the XIC selection (peak selection, XIC integration width or offset) using the controls in the right-most panel. The file will automatically reprocess as defined in the workflow. The right-most area also contains controls for displaying deuterium distributions, and extracting raw values (see lower-right hand portion of the figure).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 8: Manual assessment and validation in Hydra. The 'Manual assessment and validation' tool allows inspection and adjustment of individual experiments. Shown here is the replicate viewing mode, selected in the top left. XIC's and MS spectra from replicates are vertically aligned, to aid detection of anomalies. In this example, a particular peptide is selected from the project tree on the left. The XICs (left-most graphs) are very similar, while the second MS spectrum is different from the others. The user can then adjust the XIC selection (peak selection, XIC integration width or offset) using the controls in the right-most panel. The file will automatically reprocess as defined in the workflow. The right-most area also contains controls for displaying deuterium distributions, and extracting raw values (see lower-right hand portion of the figure).
Mentions: Hydra also provides a means for 'drilling down' to allow visual assessment, manual validation and reprocessing of individual replicates. Fig. 8 shows a screenshot of the 'Manual Assessment and Validation' form, whose arrangement resembles that of Hydra's main display: the left-side for navigation, the center for XIC and MS graphs. The right-side contains controls for adjusting the individual replicates (see below). There are three viewing modes: 'quick view' for viewing single replicates; 'replicate view' for vertically displaying all replicates of a given protein state/labeling condition/peptide/fragment (as shown in Fig. 8); and 'Protein state compare view' for vertically comparing data across protein states.

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