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Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data.

Jaitly N, Mayampurath A, Littlefield K, Adkins JN, Anderson GA, Smith RD - BMC Bioinformatics (2009)

Bottom Line: Because of the inherent complexity of mass spectral patterns produced by these biomolecules, the analysis is significantly enhanced by using visualization capabilities to inspect and confirm results.Application of Decon2LS to deisotope different datasets obtained across different instruments yielded a high number of features that can be used to identify and quantify peptides in the biological sample.Decon2LS is an efficient software package for discovering and visualizing features in proteomics studies that require automated interpretation of mass spectra.

View Article: PubMed Central - HTML - PubMed

Affiliation: Pacific Northwest National Laboratory, Richland, WA 99352, USA. ndjaitly@cs.utoronto.ca

ABSTRACT

Background: Data generated from liquid chromatography coupled to high-resolution mass spectrometry (LC-MS)-based studies of a biological sample can contain large amounts of biologically significant information in the form of proteins, peptides, and metabolites. Interpreting this data involves inferring the masses and abundances of biomolecules injected into the instrument. Because of the inherent complexity of mass spectral patterns produced by these biomolecules, the analysis is significantly enhanced by using visualization capabilities to inspect and confirm results. In this paper we describe Decon2LS, an open-source software package for automated processing and visualization of high-resolution MS data. Drawing extensively on algorithms developed over the last ten years for ICR2LS, Decon2LS packages the algorithms as a rich set of modular, reusable processing classes for performing diverse functions such as reading raw data, routine peak finding, theoretical isotope distribution modelling, and deisotoping. Because the source code is openly available, these functionalities can now be used to build derivative applications in relatively fast manner. In addition, Decon2LS provides an extensive set of visualization tools, such as high performance chart controls.

Results: With a variety of options that include peak processing, deisotoping, isotope composition, etc, Decon2LS supports processing of multiple raw data formats. Deisotoping can be performed on an individual scan, an individual dataset, or on multiple datasets using batch processing. Other processing options include creating a two dimensional view of mass and liquid chromatography (LC) elution time features, generating spectrum files for tandem MS data, creating total intensity chromatograms, and visualizing theoretical peptide profiles. Application of Decon2LS to deisotope different datasets obtained across different instruments yielded a high number of features that can be used to identify and quantify peptides in the biological sample.

Conclusion: Decon2LS is an efficient software package for discovering and visualizing features in proteomics studies that require automated interpretation of mass spectra. Besides being easy to use, fast, and reliable, Decon2LS is also open-source, which allows developers in the proteomics and bioinformatics communities to reuse and refine the algorithms to meet individual needs.Decon2LS source code, installer, and tutorials may be downloaded free of charge at http://http:/ncrr.pnl.gov/software/.

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Related in: MedlinePlus

A screen-shot of the traditional TIC-based view in Decon2LS of dataset ShewFed028_LTQFT_1_29May05_Andro_0505-02: The top pane shows the total-ion-chromatogram for the dataset, while the bottom pane shows the mass spectrum of the scan number 2067 that is selected in the TIC pane. The bottom right pane shows details of peak finding and deisotoping operations.
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Figure 3: A screen-shot of the traditional TIC-based view in Decon2LS of dataset ShewFed028_LTQFT_1_29May05_Andro_0505-02: The top pane shows the total-ion-chromatogram for the dataset, while the bottom pane shows the mass spectrum of the scan number 2067 that is selected in the TIC pane. The bottom right pane shows details of peak finding and deisotoping operations.

Mentions: Two main forms of visualization are provided to navigate datasets and the results generated. The first is a "traditional" view (Figure 3) where the total ion chromatogram for the analysis is displayed in a navigation pane on the top and is linked with the mass spectrum for a chosen scan on the bottom pane. By right-clicking on the bottom pane, one can choose the desired operations. For example, the results from deisotoping a single scan (Figure 4) can be viewed by clicking on any of the transformed records. The results include details such as the overlap of theoretical and observed spectrum, the charge state of the ion, the molecular formula generated by Averagine, and the monoisotopic peak. Options also are available to view and process contiguous spectra summed across a specified window.


Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data.

Jaitly N, Mayampurath A, Littlefield K, Adkins JN, Anderson GA, Smith RD - BMC Bioinformatics (2009)

A screen-shot of the traditional TIC-based view in Decon2LS of dataset ShewFed028_LTQFT_1_29May05_Andro_0505-02: The top pane shows the total-ion-chromatogram for the dataset, while the bottom pane shows the mass spectrum of the scan number 2067 that is selected in the TIC pane. The bottom right pane shows details of peak finding and deisotoping operations.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2666663&req=5

Figure 3: A screen-shot of the traditional TIC-based view in Decon2LS of dataset ShewFed028_LTQFT_1_29May05_Andro_0505-02: The top pane shows the total-ion-chromatogram for the dataset, while the bottom pane shows the mass spectrum of the scan number 2067 that is selected in the TIC pane. The bottom right pane shows details of peak finding and deisotoping operations.
Mentions: Two main forms of visualization are provided to navigate datasets and the results generated. The first is a "traditional" view (Figure 3) where the total ion chromatogram for the analysis is displayed in a navigation pane on the top and is linked with the mass spectrum for a chosen scan on the bottom pane. By right-clicking on the bottom pane, one can choose the desired operations. For example, the results from deisotoping a single scan (Figure 4) can be viewed by clicking on any of the transformed records. The results include details such as the overlap of theoretical and observed spectrum, the charge state of the ion, the molecular formula generated by Averagine, and the monoisotopic peak. Options also are available to view and process contiguous spectra summed across a specified window.

Bottom Line: Because of the inherent complexity of mass spectral patterns produced by these biomolecules, the analysis is significantly enhanced by using visualization capabilities to inspect and confirm results.Application of Decon2LS to deisotope different datasets obtained across different instruments yielded a high number of features that can be used to identify and quantify peptides in the biological sample.Decon2LS is an efficient software package for discovering and visualizing features in proteomics studies that require automated interpretation of mass spectra.

View Article: PubMed Central - HTML - PubMed

Affiliation: Pacific Northwest National Laboratory, Richland, WA 99352, USA. ndjaitly@cs.utoronto.ca

ABSTRACT

Background: Data generated from liquid chromatography coupled to high-resolution mass spectrometry (LC-MS)-based studies of a biological sample can contain large amounts of biologically significant information in the form of proteins, peptides, and metabolites. Interpreting this data involves inferring the masses and abundances of biomolecules injected into the instrument. Because of the inherent complexity of mass spectral patterns produced by these biomolecules, the analysis is significantly enhanced by using visualization capabilities to inspect and confirm results. In this paper we describe Decon2LS, an open-source software package for automated processing and visualization of high-resolution MS data. Drawing extensively on algorithms developed over the last ten years for ICR2LS, Decon2LS packages the algorithms as a rich set of modular, reusable processing classes for performing diverse functions such as reading raw data, routine peak finding, theoretical isotope distribution modelling, and deisotoping. Because the source code is openly available, these functionalities can now be used to build derivative applications in relatively fast manner. In addition, Decon2LS provides an extensive set of visualization tools, such as high performance chart controls.

Results: With a variety of options that include peak processing, deisotoping, isotope composition, etc, Decon2LS supports processing of multiple raw data formats. Deisotoping can be performed on an individual scan, an individual dataset, or on multiple datasets using batch processing. Other processing options include creating a two dimensional view of mass and liquid chromatography (LC) elution time features, generating spectrum files for tandem MS data, creating total intensity chromatograms, and visualizing theoretical peptide profiles. Application of Decon2LS to deisotope different datasets obtained across different instruments yielded a high number of features that can be used to identify and quantify peptides in the biological sample.

Conclusion: Decon2LS is an efficient software package for discovering and visualizing features in proteomics studies that require automated interpretation of mass spectra. Besides being easy to use, fast, and reliable, Decon2LS is also open-source, which allows developers in the proteomics and bioinformatics communities to reuse and refine the algorithms to meet individual needs.Decon2LS source code, installer, and tutorials may be downloaded free of charge at http://http:/ncrr.pnl.gov/software/.

Show MeSH
Related in: MedlinePlus