Biological MS Data and Software Distribution Center at PNNL

Decon2LS

Decon2LS is a software package used for detecting features in MS data by using the isotopic signatures of expected components. The tool uses different algorithms for different parts of the deconvolution process: noise reduction, peak detection, prediction of theoretical isotopic envelope and scoring functions that quantitate the quality of signature observed in the data. Also available as a part of the software is a rich toolkit of high performance line and scatter chart controls in .NET and controls for visualization of mass spectra.

Decon2LS can read the following file formats. However, some of the file formats require that you install the vendor-supplied data browsing software so that Decon2LS has access to the necessary DLLs.

  • mzXML files
  • Thermo Finnigan .Raw files (requires Xcalibur).
  • Agilent .Wiff files (requirs Analyst)
  • Micromass files (requires MassLynx)
  • Bruker acqu files

The "Data Extraction and Analysis for LC-MS Based Proteomics" sessions at the 2007 and 2008 US HUPO conferences discussed the use of Decon2LS for processing example LC-MS datasets to allow VIPER to match the data to an AMT tag database. PDF files of the slides presented are available for download as a 5 MB PDF file (2007) and a 6.5 MB PDF file (2008). See also the Open Source Tools for the Accurate Mass and Time (AMT) Tag Proteomics Pipeline poster presented by Navdeep Jaitly at ASMS 2006. This poster presents an overview of Decon2LS and its interactions with other proteomics software.

The source code for Decon2LS is fairly large, but includes a reasonable amount of in-code documentation. If you make any improvements to the algorithms used by Decon2LS, we would encourage you to send the updated code to us at proteomics@pnl.gov

Download Software Tool Download Tutorial Download Source Code

Software Details
Version v1.0.2964 Requirements Microsoft NET Framework 1.1
Date Updated February 12, 2008 File Size (Software Tool) 4.5 MB (ZIP)
Registration Required No File size (Source Code) 106 MB (ZIP)
Developers Navdeep Jaitly; Anoop Mayampurath; Kyle Littlefield
Comments See the complete Revision History for a history of changes


Acknowledgment

All publications that utilize this software should provide appropriate acknowledgement to PNNL and the OMICS.PNL.GOV website. However, if the software is extended or modified, then any subsequent publications should include a more extensive statement, using this text or a similar variant:

Portions of this research were supported by the NIH National Center for Research Resources (Grant RR018522), the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at PNNL), and the National Institute of Allergy and Infectious Diseases (NIH/DHHS through interagency agreement Y1-AI-4894-01). PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RL0 1830.

Decon2LS Feature Tour

View mass spectra and TIC with peak labels

Mass Spectra and TIC plots

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Allows users to view raw data from different instruments and vendors in the form of mass spectra and total ion chromatograms (TICs). Mass spectra of various scans can be seen one at a time with peak labels. It is also possible to easily zoom into specific regions of interest on the plots.

 

The Property Editor

Property Editor

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Appearance of the GUI and plots can be easily altered to personal preferences through the use of the Property Editor.

 

Horn Mass Transform Results

Horn Mass Transform Results

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Datasets can be de-isotoped through the use of the THRASH algorithm, either scan-by-scan or all at once. Horn Mass transform results are published in a table format. Parameters used for peak picking and for Horn Mass Transform can also be changed.

 

Isotopic Distribution Detail

Charge state and delta m/z on plots

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The distance between consecutive peaks of an isotopic distribution are indicated on the mass spectra, along with the charge state of the isotopic distribution's most abundant peak.

 

Heat maps of de-isotoped data

Heat Map and Elution Profile

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Heat map (scan# vs. m/z) of the peptide intensities and an elution profile (scan# vs. intensity) at a specific m/z value can be viewed for de-isotoped datasets.

 

Theoretical spectra of known compounds

Mercury Window

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The Mercury algorithm is used to generate a theoretical spectra of a compound upon entering its molecular formula. Optionally, the theoretical spectra can be overlaid on top of an experimental mass spectrum.

 

Isotopic composition of over 100 elements

Isotopic composition

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The isotopic composition of over a hundred elements are provided in a table format and can be saved as an .XML file. The loaded isotopic composition values are used by the Mercury algorithm to generate a theoretical isotopic distribution of a detected peptide.