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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

The variant of the THRASH algorithm used in Decon2LS: peaks in the mass spectrum are found by comparing their intensity to their shoulders and to the background. Starting at the most intense peak deisotoping is performed by determining charge state, estimating empirical formula, generating a theoretical profile, scoring the theoretical profile and deleting points from the spectrum. This process is continued while peaks of intensity greater than a user specified threshold ratio of the background still exist.
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Figure 2: The variant of the THRASH algorithm used in Decon2LS: peaks in the mass spectrum are found by comparing their intensity to their shoulders and to the background. Starting at the most intense peak deisotoping is performed by determining charge state, estimating empirical formula, generating a theoretical profile, scoring the theoretical profile and deleting points from the spectrum. This process is continued while peaks of intensity greater than a user specified threshold ratio of the background still exist.

Mentions: The THRASH algorithm uses modules to determine peak charge states (the autocorrelation algorithm [16]), generate theoretical profiles (the Mercury algorithm [2]) and to score theoretical profiles against observed patterns. Decon2LS implements a derivative of the THRASH algorithm, using the same components, but with different scoring schemes. Indexing and caching algorithms (described below) are also used internally to optimize algorithm performance. The steps performed by the THRASH algorithm variant used in Decon2LS are depicted in Figure 2, and described further in the text that follows. Note that the algorithm can either be run interactively on an individual mass spectrum or in a batch mode on all the mass spectra in a dataset using the Process form available in the application.


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 variant of the THRASH algorithm used in Decon2LS: peaks in the mass spectrum are found by comparing their intensity to their shoulders and to the background. Starting at the most intense peak deisotoping is performed by determining charge state, estimating empirical formula, generating a theoretical profile, scoring the theoretical profile and deleting points from the spectrum. This process is continued while peaks of intensity greater than a user specified threshold ratio of the background still exist.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: The variant of the THRASH algorithm used in Decon2LS: peaks in the mass spectrum are found by comparing their intensity to their shoulders and to the background. Starting at the most intense peak deisotoping is performed by determining charge state, estimating empirical formula, generating a theoretical profile, scoring the theoretical profile and deleting points from the spectrum. This process is continued while peaks of intensity greater than a user specified threshold ratio of the background still exist.
Mentions: The THRASH algorithm uses modules to determine peak charge states (the autocorrelation algorithm [16]), generate theoretical profiles (the Mercury algorithm [2]) and to score theoretical profiles against observed patterns. Decon2LS implements a derivative of the THRASH algorithm, using the same components, but with different scoring schemes. Indexing and caching algorithms (described below) are also used internally to optimize algorithm performance. The steps performed by the THRASH algorithm variant used in Decon2LS are depicted in Figure 2, and described further in the text that follows. Note that the algorithm can either be run interactively on an individual mass spectrum or in a batch mode on all the mass spectra in a dataset using the Process form available in the application.

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