Abstract
During the past decade, the field of mass spectrometry imaging (MSI) has greatly evolved, to a point where it has now been fully integrated by most vendors as an optional or dedicated platform that can be purchased with their instruments. However, the technology is not mature and multiple research groups in both academia and industry are still very actively studying the fundamentals of imaging techniques, adapting the technology to new ionization sources, and developing new applications. As a result, there important varieties of data file formats used to store mass spectrometry imaging data and, concurrent to the development of MSi, collaborative efforts have been undertaken to introduce common imaging data file formats. However, few free software packages to read and analyze files of these different formats are readily available. We introduce here MSiReader, a free open source application to read and analyze high resolution MSI data from the most common MSi data formats. The application is built on the Matlab platform (Mathworks, Natick, MA, USA) and includes a large selection of data analysis tools and features. People who are unfamiliar with the Matlab language will have little difficult navigating the user-friendly interface, and users with Matlab programming experience can adapt and customize MSiReader for their own needs.
References
Stoeckli, M., Staab, D., Staufenbiel, M., Wiederhold, K.H., Signor, L.: Molecular imaging of amyloid beta peptides in mouse brain sections using mass spectrometry. Anal. Biochem. 311(1), 33–39 (2002)
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(3), 332–345 (2008)
Hester, A.B., Bouschen, W., Leisner, A., Maass, K., Paschke, C., Spengler, B.: Proc. 53rd ASMS Conf Mass Spectrom Allied Top, San Antonio, Tx, June 05–09 (2005)
Smith, D.F., Kharchenko, A., Konijnenburg, M., Klinkert, I., Pasa-Tolic, L., Heeren, R.M.: Advanced mass calibration and visualization for FT-ICR mass spectrometry imaging. J. Am. Soc. Mass Spectrom. 23(12), 1865–1872 (2012)
msimaging: http://www.maldi-msi.org/. Accessed 22 Dec 2012
Robichaud, G., Barry, J., Garrard, K., Muddiman, D.: Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) imaging source coupled to a FT-ICR mass spectrometer. J. Am. Soc. Mass Spectrom. 24(1), 92–100 (2013)
Pedrioli, P.G., Eng, J.K., Hubley, R., Vogelzang, M., Deutsch, E.W., Raught, B., Pratt, B., Nilsson, E., Angeletti, R.H., Apweiler, R., Cheung, K., Costello, C.E., Hermjakob, H., Huang, S., Julian, R.K., Kapp, E., McComb, M.E., Oliver, S.G., Omenn, G., Paton, N.W., Simpson, R., Smith, R., Taylor, C.F., Zhu, W., Aebersold, R.: A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol. 22(11), 1459–1466 (2004)
ProteoWizard: http://proteowizard.sourceforge.net/. Accessed 22 Dec 2012
Kessner, D., Chambers, M., Burke, R., Agus, D., Mallick, P.: ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 24(21), 2534–2536 (2008)
mzXML converter: http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML. Accessed 22 Dec 2012
Römpp, A., Schramm, T., Hester, A., Klinkert, I., Heeren, R., Stöckli, M., Both, J.-P., Brunelle, A., Spengler, B.: Data mining in proteomics. Humana Press, New York (2010)
Schramm, T., Hester, A., Klinkert, I., Both, J.P., Heeren, R.M., Brunelle, A., Laprevote, O., Desbenoit, N., Robbe, M.F., Stoeckli, M., Spengler, B., Rompp, A.: imzML—a common data format for the flexible exchange and processing of mass spectrometry imaging data. J. Proteom. 75(16), 5106–5110 (2012)
Martens, L., Chambers, M., Sturm, M., Kessner, D., Levander, F., Shofstahl, J., Tang, W.H., Rompp, A., Neumann, S., Pizarro, A.D., Montecchi-Palazzi, L., Tasman, N., Coleman, M., Reisinger, F., Souda, P., Hermjakob, H., Binz, P.A., Deutsch, E.W.: mzML—a community standard for mass spectrometry data. Mol. Cell. Proteom. 10(1), R110 000133 (2011)
Race, A.M., Styles, I.B., Bunch, J.: Inclusive sharing of mass spectrometry imaging data requires a converter for all. J. Proteom. 75(16), 5111–5112 (2012)
Analyze 7.5: http://eeg.sourceforge.net/. Accessed 22 Dec 2012
McDonnell, L.A., van Remoortere, A., de Velde, N., van Zeijl, R.J.M., Deelder, A.M.: Imaging mass spectrometry data reduction: automated feature identification and extraction. J. Am. Soc. Mass Spectrom. 21(12), 1969–1978 (2010)
Sud, M., Fahy, E., Cotter, D., Brown, A., Dennis, E.A., Glass, C.K., Merrill Jr., A.H., Murphy, R.C., Raetz, C.R., Russell, D.W., Subramaniam, S.L.M.S.D.: LIPID MAPS structure database. Nucleic Acids Res. 35(Database issue), D527–532 (2007)
LIPID MAPS Structure Database (LDMS): http://www.lipidmaps.org/data/structure/index.html. Accessed 22 Dec 2012
Giancaspro, C., Comisarow, M.B.: Exact interpolation of Fourier-transform spectra. Appl. Spectrosc. 37(2), 153–166 (1983)
Jones, E.A., Deininger, S.O., Hogendoorn, P.C., Deelder, A.M., McDonnell, L.A.: Imaging mass spectrometry statistical analysis. J. Proteom. 75(16), 4962–4989 (2012)
Open Source Initiative OSI - The BSD 3-Clause License: http://opensource.org/licenses/BSD-3-Clause. Accessed 22 Dec 2012
Acknowledgments
The authors thank Alan M. Race from the University of Birmingham for granting them permission to include his imzML parser function [14] in MSiReader. The authors gratefully acknowledge the financial support received from the National Institutes of Health (R01GM087964), the W. M. Keck Foundation, and North Carolina State University.
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Robichaud, G., Garrard, K.P., Barry, J.A. et al. MSiReader: An Open-Source Interface to View and Analyze High Resolving Power MS Imaging Files on Matlab Platform. J. Am. Soc. Mass Spectrom. 24, 718–721 (2013). https://doi.org/10.1007/s13361-013-0607-z
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DOI: https://doi.org/10.1007/s13361-013-0607-z