OmniSpect: An Open MATLAB-Based Tool for Visualization and Analysis of Matrix-Assisted Laser Desorption/Ionization and Desorption Electrospray Ionization Mass Spectrometry Images

  • R. Mitchell Parry
  • Asiri S. Galhena
  • Chaminda M. Gamage
  • Rachel V. Bennett
  • May D. WangEmail author
  • Facundo M. FernándezEmail author
Application Note


We present omniSpect, an open source web- and MATLAB-based software tool for both desorption electrospray ionization (DESI) and matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging (MSI) that performs computationally intensive functions on a remote server. These functions include converting data from a variety of file formats into a common format easily manipulated in MATLAB, transforming time-series mass spectra into mass spectrometry images based on a probe spatial raster path, and multivariate analysis. OmniSpect provides an extensible suite of tools to meet the computational requirements needed for visualizing open and proprietary format MSI data.

Key words

Mass spectrometry imaging Desorption electrospray ionization (DESI) Matrix-assisted laser desorption ionization (MALDI) Data processing Multivariate image analysis Web-based tool Software MATLAB 



The authors acknowledge support from ARRA NSF MRI Instrument Development grant no. 0923179 to FMF and MDW. This research was also supported by NIH grant U54CA119338, a Georgia Cancer Coalition Distinguished Cancer Scholar Award to Professor MDW, Hewlett Packard, and Microsoft Research.We would also like to thank Al Merrill, Cameron Sullards and Frank Chen for useful suggestions during the development of this software.

Supplementary material

13361_2012_572_MOESM1_ESM.doc (78 kb)
ESM 1 (DOC 77 kb)


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Copyright information

© American Society for Mass Spectrometry 2013

Authors and Affiliations

  • R. Mitchell Parry
    • 1
  • Asiri S. Galhena
    • 2
  • Chaminda M. Gamage
    • 2
  • Rachel V. Bennett
    • 2
  • May D. Wang
    • 3
    Email author
  • Facundo M. Fernández
    • 2
    Email author
  1. 1.The Wallace H. Coulter Department of Biomedical EngineeringEmory UniversityAtlantaUSA
  2. 2.The Georgia Institute of TechnologyAtlantaUSA
  3. 3.The Wallace H. Coulter Department of Biomedical Engineering, Department of Electrical and Computer Engineering, Winship Cancer Institute, Parker H. Petit Institute of Bioengineering and BiosciencesGeorgia Institute of Technology and Emory UniversityAtlantaUSA

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