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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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Primary layout of Hydra for viewing data output. The example provides a table of the averaged deuterium incorporation values for two protein states, along with and other statistical measures. The screen is divided into three areas. The left-most area is used for navigating: the 'data' tab shows the project tree, the 'peptides' tab lists the peptide data set and the 'results' tab allows the user to navigate various views of the data. The center displays results in either tabular of graphical form, where the inset shows a 'chart' view of deuteration values for the two protein states (red and blue), zoomed into particular range of peptides. The right-most area shows detailed context-sensitive properties.
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Figure 6: Primary layout of Hydra for viewing data output. The example provides a table of the averaged deuterium incorporation values for two protein states, along with and other statistical measures. The screen is divided into three areas. The left-most area is used for navigating: the 'data' tab shows the project tree, the 'peptides' tab lists the peptide data set and the 'results' tab allows the user to navigate various views of the data. The center displays results in either tabular of graphical form, where the inset shows a 'chart' view of deuteration values for the two protein states (red and blue), zoomed into particular range of peptides. The right-most area shows detailed context-sensitive properties.

Mentions: Fig. 6 shows the primary layout of Hydra as it is used in viewing the processed data. The screen is divided into three sections. The left-most section is used for navigating through the project tree, including protein states, labeling conditions and individual peptides. The center area displays graphs and tables of data and the right-most section presents context-sensitive properties of the selected feature of the project tree. The primary means of viewing deuterium incorporation data is through the summary table, shown in the center section of Fig. 6. This table reports the averaged deuterium incorporation values and their standard deviations for the replicates for each peptide of each protein state. In the sample table of Fig. 6, we compare the apo versus holo forms of calmodulin. Comparative statistics are shown in the right-most columns of the table. These include the deuteration ratio and its standard deviation, a Student's t-test and P-value for detecting differences between the two protein states. Right-clicking on the table allows the user to control the selection of protein states being compared. A graphical view of the data is also shown in the screenshot overlaying the table.


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)

Primary layout of Hydra for viewing data output. The example provides a table of the averaged deuterium incorporation values for two protein states, along with and other statistical measures. The screen is divided into three areas. The left-most area is used for navigating: the 'data' tab shows the project tree, the 'peptides' tab lists the peptide data set and the 'results' tab allows the user to navigate various views of the data. The center displays results in either tabular of graphical form, where the inset shows a 'chart' view of deuteration values for the two protein states (red and blue), zoomed into particular range of peptides. The right-most area shows detailed context-sensitive properties.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Primary layout of Hydra for viewing data output. The example provides a table of the averaged deuterium incorporation values for two protein states, along with and other statistical measures. The screen is divided into three areas. The left-most area is used for navigating: the 'data' tab shows the project tree, the 'peptides' tab lists the peptide data set and the 'results' tab allows the user to navigate various views of the data. The center displays results in either tabular of graphical form, where the inset shows a 'chart' view of deuteration values for the two protein states (red and blue), zoomed into particular range of peptides. The right-most area shows detailed context-sensitive properties.
Mentions: Fig. 6 shows the primary layout of Hydra as it is used in viewing the processed data. The screen is divided into three sections. The left-most section is used for navigating through the project tree, including protein states, labeling conditions and individual peptides. The center area displays graphs and tables of data and the right-most section presents context-sensitive properties of the selected feature of the project tree. The primary means of viewing deuterium incorporation data is through the summary table, shown in the center section of Fig. 6. This table reports the averaged deuterium incorporation values and their standard deviations for the replicates for each peptide of each protein state. In the sample table of Fig. 6, we compare the apo versus holo forms of calmodulin. Comparative statistics are shown in the right-most columns of the table. These include the deuteration ratio and its standard deviation, a Student's t-test and P-value for detecting differences between the two protein states. Right-clicking on the table allows the user to control the selection of protein states being compared. A graphical view of the data is also shown in the screenshot overlaying the table.

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