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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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The Mercury form provides an implementation of the Mercury algorithm to allow users to generate theoretical isotopic distribution for any compound on the basis of the elemental isotopic distribution using user specified parameters for charge state, resolution and type of peak shape. In this figure we show the theoretical isotope pattern of C113 H184 N28 O24 with charge of 1 generated at a resolution of 100,000.
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Figure 6: The Mercury form provides an implementation of the Mercury algorithm to allow users to generate theoretical isotopic distribution for any compound on the basis of the elemental isotopic distribution using user specified parameters for charge state, resolution and type of peak shape. In this figure we show the theoretical isotope pattern of C113 H184 N28 O24 with charge of 1 generated at a resolution of 100,000.

Mentions: Decon2LS includes a number of other data processing features. For example, the Mercury algorithm can be used to view the theoretical spectrum of any peptide sequence or atomic formulae at different charge states and instrument resolution (Figure 6). Decon2LS also creates TIC plots from the Scan summary file. Additionally, the software can be used to process tandem MS results by using the DeconMSn algorithm to create ".dta" spectrum files for a given LC-MS/MS dataset [21]. These files can be processed using search-engines such as SEQUEST[22] to identify peptides.


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)

The Mercury form provides an implementation of the Mercury algorithm to allow users to generate theoretical isotopic distribution for any compound on the basis of the elemental isotopic distribution using user specified parameters for charge state, resolution and type of peak shape. In this figure we show the theoretical isotope pattern of C113 H184 N28 O24 with charge of 1 generated at a resolution of 100,000.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: The Mercury form provides an implementation of the Mercury algorithm to allow users to generate theoretical isotopic distribution for any compound on the basis of the elemental isotopic distribution using user specified parameters for charge state, resolution and type of peak shape. In this figure we show the theoretical isotope pattern of C113 H184 N28 O24 with charge of 1 generated at a resolution of 100,000.
Mentions: Decon2LS includes a number of other data processing features. For example, the Mercury algorithm can be used to view the theoretical spectrum of any peptide sequence or atomic formulae at different charge states and instrument resolution (Figure 6). Decon2LS also creates TIC plots from the Scan summary file. Additionally, the software can be used to process tandem MS results by using the DeconMSn algorithm to create ".dta" spectrum files for a given LC-MS/MS dataset [21]. These files can be processed using search-engines such as SEQUEST[22] to identify peptides.

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