Limits...
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.

Show MeSH

Related in: MedlinePlus

H/DX-MS and HDX-MS/MS data processing.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2696453&req=5

Figure 1: H/DX-MS and HDX-MS/MS data processing.

Mentions: Two packages are available that operate on a project-wide scale. The Deuterator [11], is a freely available web-based tool that organizes the raw data files according to experimental conditions, and effectively completes all the tasks in the MS-based workflow shown in Fig. 1. As with AutoHD, It uses a 'theoretical fit method' to measure deuterium incorporation, in which the theoretical isotopic profile for varying degrees of deuterium labeling is fit to the experimental isotopic profile. Deuterium incorporation values can be outputted and further data handling is left to the researcher. A newer version, 'HD Desktop' [12], provides additional data handling capabilities. 'TOF2H' is a second package [13]. This is a recently published Excel-based application geared toward processing and viewing MS-level MALDI-TOF data from the AB 4700 TOF-TOF instrument. TOF2H organizes raw files, and iterates through the typical processing workflow shown on the left-hand side of Fig. 1. Other packages have been described in the literature, but are not as readily available [14,15].


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)

H/DX-MS and HDX-MS/MS data processing.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: H/DX-MS and HDX-MS/MS data processing.
Mentions: Two packages are available that operate on a project-wide scale. The Deuterator [11], is a freely available web-based tool that organizes the raw data files according to experimental conditions, and effectively completes all the tasks in the MS-based workflow shown in Fig. 1. As with AutoHD, It uses a 'theoretical fit method' to measure deuterium incorporation, in which the theoretical isotopic profile for varying degrees of deuterium labeling is fit to the experimental isotopic profile. Deuterium incorporation values can be outputted and further data handling is left to the researcher. A newer version, 'HD Desktop' [12], provides additional data handling capabilities. 'TOF2H' is a second package [13]. This is a recently published Excel-based application geared toward processing and viewing MS-level MALDI-TOF data from the AB 4700 TOF-TOF instrument. TOF2H organizes raw files, and iterates through the typical processing workflow shown on the left-hand side of Fig. 1. Other packages have been described in the literature, but are not as readily available [14,15].

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