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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 figure shows a zoomed in view of scan # 9520 in dataset ShewFed028_LTQFT_1_29May05_Andro_0505-02 where two different chemical species produce isotopic peaks that overlap. Decon2LS draws line between isotopic peaks of the same species and shows how the two species were successfully deisotoped.
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Figure 7: The figure shows a zoomed in view of scan # 9520 in dataset ShewFed028_LTQFT_1_29May05_Andro_0505-02 where two different chemical species produce isotopic peaks that overlap. Decon2LS draws line between isotopic peaks of the same species and shows how the two species were successfully deisotoped.

Mentions: A common occurrence while deisotoping a mass spectrum is that two or more peptides have overlapping isotopic patterns, which can result in poor fitness scores. The ability of Decon2LS to accurately determine the monoisotopic mass of two overlapping species whose peaks overlap with one another is exemplified in Figure 7. In this example two isotopic distributions are detected; a 2201.233 Da species at charge state 2 and a 3300.725 Da species at charge state 3. These two species resulted in two isotopic peaks separated by only 0.044 m/z units, as can be seen in Figure 7 the result is two partially overlapping peaks. While not perfect, the ability to resolve overlapping patterns is enhanced by the sequence in which deisotoping attempts are performed by the algorithm. For example, peaks are processed in order of descending intensity, so the highest peak of an overlapping isotopic distribution is processed first. However, during the first attempt, the fitness score may be too low. In this case, the algorithm proceeds to deisotope other patterns in the spectrum. Once Decon2LS succeeds in processing one of the overlapping patterns, the software removes the processed peak from the spectrum. At this point, the process of deisotoping the original pattern starts over at one of the remaining isotopic peaks, and after "THRASHing" the best match between the theoretical pattern and the remaining observed pattern is determined. Developing methods to tag overlapping isotopic patterns and fit them using least-squares based procedures, such as those described elsewhere [24] may further improve algorithm performance.


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 figure shows a zoomed in view of scan # 9520 in dataset ShewFed028_LTQFT_1_29May05_Andro_0505-02 where two different chemical species produce isotopic peaks that overlap. Decon2LS draws line between isotopic peaks of the same species and shows how the two species were successfully deisotoped.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 7: The figure shows a zoomed in view of scan # 9520 in dataset ShewFed028_LTQFT_1_29May05_Andro_0505-02 where two different chemical species produce isotopic peaks that overlap. Decon2LS draws line between isotopic peaks of the same species and shows how the two species were successfully deisotoped.
Mentions: A common occurrence while deisotoping a mass spectrum is that two or more peptides have overlapping isotopic patterns, which can result in poor fitness scores. The ability of Decon2LS to accurately determine the monoisotopic mass of two overlapping species whose peaks overlap with one another is exemplified in Figure 7. In this example two isotopic distributions are detected; a 2201.233 Da species at charge state 2 and a 3300.725 Da species at charge state 3. These two species resulted in two isotopic peaks separated by only 0.044 m/z units, as can be seen in Figure 7 the result is two partially overlapping peaks. While not perfect, the ability to resolve overlapping patterns is enhanced by the sequence in which deisotoping attempts are performed by the algorithm. For example, peaks are processed in order of descending intensity, so the highest peak of an overlapping isotopic distribution is processed first. However, during the first attempt, the fitness score may be too low. In this case, the algorithm proceeds to deisotope other patterns in the spectrum. Once Decon2LS succeeds in processing one of the overlapping patterns, the software removes the processed peak from the spectrum. At this point, the process of deisotoping the original pattern starts over at one of the remaining isotopic peaks, and after "THRASHing" the best match between the theoretical pattern and the remaining observed pattern is determined. Developing methods to tag overlapping isotopic patterns and fit them using least-squares based procedures, such as those described elsewhere [24] may further improve algorithm performance.

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