Advertisement

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

Abstract

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 

Notes

Acknowledgment

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)

References

  1. 1.
    Hayasaka, T., Goto-Inoue, N., Ushijima, M., Yao, I.K.K., Yuba-Kubo, A., Wakui, M., Kajihara, S., Matsuura, M., Setou, M.: Development of Imaging Mass Spectrometry (IMS) Dataset Extractor Software, IMS Convolution. Anal. Bioanal. Chem. 401, 183–193 (2011)CrossRefGoogle Scholar
  2. 2.
    Jardin-Mathe, O., Bonnel, D., Franck, J., Wisztorski, M., Macagno, E., Fournier, I., Salzet, M.: MITICS (MALDI Imaging Team Imaging Computing System): a new open source mass spectrometry imaging software. J. Proteom. 71, 332–345 (2008)CrossRefGoogle Scholar
  3. 3.
    Klinkert, I., McDonnell, L.A., Luxembourg, S.L., Altelaar, A.F.M., Amstalden, E.R., Piersma, S.R., Heeren, R.M.A.: Tools and strategies for visualization of large image data sets in high-resolution imaging mass spectrometry. Rev. Sci. Instrum. 78, 053716 (2007)CrossRefGoogle Scholar
  4. 4.
    Shimma, S., Sugiura, Y., Hayasaka, T., Zaima, N., Matsumoto, M., Setou, M.: Mass imaging and identification of biomolecules with MALDI-QIT-TOF-Based System. Anal. Chem. 80, 878–885 (2008)CrossRefGoogle Scholar
  5. 5.
    Zhang, F.Q., Hong, D.: Elastic net-based framework for imaging mass spectrometry data biomarker selection and classification. Stat. Med. 30, 753–768 (2011)CrossRefGoogle Scholar
  6. 6.
    Zimmerman, T.A., Debois, D., Mazzucchelli, G., Bertrand, V., De Pauw-Gillet, M.C., De Pauw, E.: An analytical pipeline for MALDI in-source decay mass spectrometry imaging. Anal. Chem. 83, 6090–6097 (2011)CrossRefGoogle Scholar
  7. 7.
    Svatos, A.: Mass spectrometric imaging of small molecules. Trends Biotechnol. 28, 425–434 (2010)CrossRefGoogle Scholar
  8. 8.
    Bruand, J., Alexandrov, T., Sistla, S., Wisztorski, M., Meriaux, C., Becker, M., Salzet, M., Fournier, I., Macagno, E., Bafna, V.: AMASS: Algorithm for MSI analysis by semi-supervised segmentation. J. Proteome Res. 10, 4734–4743 (2011)CrossRefGoogle Scholar
  9. 9.
    Liu, N.A., Liu, F., Xu, B., Gao, Y.B., Li, X.H., Wei, K.H., Zhang, X.M., Yang, S.C.: Establishment of imaging mass spectrometry of biological tissues and its application on the proteome analysis of microwave radiated rat hippocampus. Chin. J. Anal. Chem. 36, 421–425 (2008)CrossRefGoogle Scholar
  10. 10.
    Ohlhausen, J.A.T., Keenan, M.R., Kotula, P.G., Peebles, D.E.: Multivariate statistical analysis of time-of-flight secondary ion mass spectrometry images using AXSIA. Appl. Surf. Sci. 231, 230–234 (2004)CrossRefGoogle Scholar
  11. 11.
    Parry, R.M., Galhena, A., Fernandex, F., Wang, M.D.: Deblurring molecular images using desorption electrospray ionization mass spectrometry. Proc. of 31st Annual Int. Conf. of the IEEE Engineering in Medicine and Biology Society (EMBC’09). 6731–6734, Minneapolis, MN (2009)Google Scholar
  12. 12.
    Galhena, A.S., Harris, G.A., Kwasnik, M., Fernandez, F.M.: Enhanced direct ambient analysis by differential mobility-filtered desorption electrospray ionization-mass spectrometry. Anal. Chem. 82, 9159–9163 (2010)CrossRefGoogle Scholar
  13. 13.
    Lee, D.D., Seung, H.S.: Learning the parts of objects by non-negative matrix factorization. Nature 401, 788–791 (1999)CrossRefGoogle Scholar
  14. 14.
    Cichocki, A.: Nonnegative matrix and tensor factorizations: applications to exploratory multi-way data analysis and blind source separation. Wiley, Chichester (2009)CrossRefGoogle Scholar
  15. 15.
    Tauler, R.: Multivariate curve resolution applied to second order data. Chemom. Intell. Lab. Syst. 30, 133–146 (1995)CrossRefGoogle Scholar
  16. 16.
    Lee, J.L.S., Gilmore, I.S., Seah, M.P.: Quantification and methodology issues in multivariate analysis of ToF-SIMS data for mixed organic systems. Surf. Interface Anal. 40, 1–14 (2008)CrossRefGoogle Scholar
  17. 17.
    Yang, L., Shirahata, N., Saini, G., Zhang, F., Pei, L., Asplund, M.C., Kurth, D.G., Ariga, K., Sautter, K., Nakanishi, T., Smentkowski, V., Linford, M.R.: Effect of surface free energy on pdms transfer in microcontact printing and its application to ToF-SIMS to probe surface energies. Langmuir 25, 5674–5683 (2009)CrossRefGoogle Scholar
  18. 18.
    Smentkowski, V.S., Ostrowski, S.G., Keenan, M.R.: A comparison of multivariate statistical analysis protocols for ToF-SIMS spectral images. Surf. Interface Anal. 41, 88–96 (2009)CrossRefGoogle Scholar
  19. 19.
    Lee, J.L.S., Gilmore, I.S., Fletcher, I.W., Seah, M.P.: Multivariate Image analysis strategies for ToF-SIMS images with topography. Surf. Interface Anal. 41, 653–665 (2009)CrossRefGoogle Scholar
  20. 20.
    Aoyagi, S., Matsuzaki, T., Takahashi, M., Sakurai, Y., Kudo, M.: Evaluation of reagent effect on skin using time-of-flight secondary ion mass spectrometry and multivariate curve resolution. Surf. Interface Anal. 44, 772–775 (2012)CrossRefGoogle Scholar
  21. 21.
    Siy, P.W., Moffitt, R.A., Parry, R.M., Chen, Y.F., Liu, Y., Sullards, M.C., Merrill, A.H., Wang, M.D.: Matrix factorization techniques for analysis of imaging mass spectrometry data. Proc. of 8th IEEE International Conference on BioInformatics and BioEngineering (BIBE’08), pp. 1–6 (2008)Google Scholar

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

Personalised recommendations