title: Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data.
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.
  
  
  CONCLUSIONS
  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/.
authors.affiliation: Pacific Northwest National Laboratory, Richland, WA 99352, USA. ndjaitly@cs.utoronto.ca
authors.forename: Navdeep
authors.initials: N
authors.lastname: Jaitly
authors.forename: Anoop
authors.initials: A
authors.lastname: Mayampurath
authors.forename: Kyle
authors.initials: K
authors.lastname: Littlefield
authors.forename: Joshua N
authors.initials: JN
authors.lastname: Adkins
authors.forename: Gordon A
authors.initials: GA
authors.lastname: Anderson
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
mesh_terms: D000465:Algorithms; D002853:Chromatography, Liquid / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods*; D040901:Proteomics / Q000379:methods; D012984:Software