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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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Inputting Peptide Data from a MASCOT search result. After selecting a Mascot search result exported in 'csv' format, the user clicks 'Process'. Hydra parses the search result and lists the protein hits. The peptide data (m/z, retention time, charge state, sequence, etc.) from the selected protein are imported into Hydra.
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Figure 3: Inputting Peptide Data from a MASCOT search result. After selecting a Mascot search result exported in 'csv' format, the user clicks 'Process'. Hydra parses the search result and lists the protein hits. The peptide data (m/z, retention time, charge state, sequence, etc.) from the selected protein are imported into Hydra.

Mentions: Hydra focuses on bottom-up H/DX-MS experiments and therefore examines deuteration incorporation at the peptide level. Minimally the researcher must supply the sequence, m/z, expected retention time, and charge state for each peptide. This can be accomplished within Hydra by parsing the Comma Separated Values (.csv) output of a Mascot search result, for example, allowing a quick way to import peptide data from a common database search program; a screenshot of this tool is shown in Fig. 3. Alternatively, the peptide data may be entered manually within Hydra or from a user-generated .csv format (i.e., using Excel.


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)

Inputting Peptide Data from a MASCOT search result. After selecting a Mascot search result exported in 'csv' format, the user clicks 'Process'. Hydra parses the search result and lists the protein hits. The peptide data (m/z, retention time, charge state, sequence, etc.) from the selected protein are imported into Hydra.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Inputting Peptide Data from a MASCOT search result. After selecting a Mascot search result exported in 'csv' format, the user clicks 'Process'. Hydra parses the search result and lists the protein hits. The peptide data (m/z, retention time, charge state, sequence, etc.) from the selected protein are imported into Hydra.
Mentions: Hydra focuses on bottom-up H/DX-MS experiments and therefore examines deuteration incorporation at the peptide level. Minimally the researcher must supply the sequence, m/z, expected retention time, and charge state for each peptide. This can be accomplished within Hydra by parsing the Comma Separated Values (.csv) output of a Mascot search result, for example, allowing a quick way to import peptide data from a common database search program; a screenshot of this tool is shown in Fig. 3. Alternatively, the peptide data may be entered manually within Hydra or from a user-generated .csv format (i.e., using Excel.

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