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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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Architecture of the Decon2LS software: Decon2LS is written using a mixture of visualization modules written in C# in the .NET programming environment, and backend libraries (DeconEngine) written in standard C++ libraries. The DeconEngine library implements modules for reading different types of vendor formats, peak finding routines, theoretical isotopic pattern generation and deisotoping. The front end talks to these libraries through wrappers written in Microsoft's Managed C++.
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Figure 1: Architecture of the Decon2LS software: Decon2LS is written using a mixture of visualization modules written in C# in the .NET programming environment, and backend libraries (DeconEngine) written in standard C++ libraries. The DeconEngine library implements modules for reading different types of vendor formats, peak finding routines, theoretical isotopic pattern generation and deisotoping. The front end talks to these libraries through wrappers written in Microsoft's Managed C++.

Mentions: The basic architecture of the Decon2LS software package is depicted in Figure 1. Written on the .NET framework, the core of Decon2LS (called the DeconEngine) is written in standard C++ using Standard Template Libraries (STL). The user interface is written in C# with a C++ wrapper that acts as the interface between front-end and back-end processing. For Windows machines, Decon2LS requires installation of the .NET framework (default for XP and higher). A separate installer that installs both Decon2LS and the .NET framework is also provided to accommodate older operating systems. Installation details and the source code are available for download free of charge at . Access to the source code allows Unix-based computer users to detach the engine and build their own wrappers and user interface. The Apache open-source license allows the original code to be modified for individual needs.


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)

Architecture of the Decon2LS software: Decon2LS is written using a mixture of visualization modules written in C# in the .NET programming environment, and backend libraries (DeconEngine) written in standard C++ libraries. The DeconEngine library implements modules for reading different types of vendor formats, peak finding routines, theoretical isotopic pattern generation and deisotoping. The front end talks to these libraries through wrappers written in Microsoft's Managed C++.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Architecture of the Decon2LS software: Decon2LS is written using a mixture of visualization modules written in C# in the .NET programming environment, and backend libraries (DeconEngine) written in standard C++ libraries. The DeconEngine library implements modules for reading different types of vendor formats, peak finding routines, theoretical isotopic pattern generation and deisotoping. The front end talks to these libraries through wrappers written in Microsoft's Managed C++.
Mentions: The basic architecture of the Decon2LS software package is depicted in Figure 1. Written on the .NET framework, the core of Decon2LS (called the DeconEngine) is written in standard C++ using Standard Template Libraries (STL). The user interface is written in C# with a C++ wrapper that acts as the interface between front-end and back-end processing. For Windows machines, Decon2LS requires installation of the .NET framework (default for XP and higher). A separate installer that installs both Decon2LS and the .NET framework is also provided to accommodate older operating systems. Installation details and the source code are available for download free of charge at . Access to the source code allows Unix-based computer users to detach the engine and build their own wrappers and user interface. The Apache open-source license allows the original code to be modified for individual needs.

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