OpenMSI: Web-based visualization, analysis and management of mass spectrometry imaging data


Mass spectrometry imaging (MSI) is widely applied to image complex samples for applications spanning health, microbial ecology, and high throughput screening of high-density arrays. MSI has emerged as a technique suited to resolving metabolism within complex cellular systems; where understanding the spatial variation of metabolism is vital for making a transformative impact on science. Unfortunately, the scale of MSI data and complexity of analysis presents an insurmountable barrier to scientists where a single 2D-image may be many gigabytes and comparison of multiple images is beyond the capabilities available to most scientists. The OpenMSI project will overcome these challenges, allowing broad use of MSI to researchers by providing a web-based gateway for management and storage of MSI data, the visualization of the hyper-dimensional contents of the data, and the statistical analysis.

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Sample: Flax (Linum usitatissimum) pod

Instrument: Waters Synapt G2 HDMS

Desorption/Ionization Method: MALDI DHB

Original File: *.imzML and *.img

Original Filesize: 15 GB

OpenMSI Filesize: 2.7 GB

Image dimensions: 303 x 291 pixels

Pixel size: 20 microns

#m/z bins: 90,000

Contributors: Doralyn S. Dalisay, Hong Yang, Laurence B. Davin and Norman G. Lewis

Sample: Potato eye stamped on NIMS chip

Instrument: AbSciex 5800

Desorption/Ionization Method: NIMS

Original File: *.img

Original Filesize: 21 GB

OpenMSI Filesize: 8.5 GB

Image dimensions: 123 x 463 pixels

Pixel size: 100 microns

#m/z bins: 188,960

Computed data: peak-finding, NMF

Contributors: Katherine Louie and Trent Northen

Sample: Leaf of transgenic hybird Poplar (Populus tremula × Populus alba)

Instrument: Waters Synapt G2 HDMS

Desorption/Ionization Method: MALDI DHB

Original File: *.img and *.imzML

Original Filesize: 4.2 GB

OpenMSI Filesize: 543 MB

Image dimensions: 213 x 173 pixels

Pixel size: 50 microns

#m/z bins: 60,000

Contributors: Costa, M.A., Marques, J.V., Dalisay, D.S., Herman, B., Bedgar, D.L., Davin, L.B. and Lewis N.G. Transgenic hybrid poplar for sustainable and scalable production of the commodity/specialty chemical, 2-phenylethanol. PLoS One, 2013 Dec 26;8(12):e83169


Sample: two microbes plated on rich LB-agar

Instrument: AbSciex 5800

Desorption/Ionization Method: NIMS

Original File: *.img

Original Filesize: 8.8 GB

OpenMSI Filesize: 1.2 GB

Image dimensions: 250 x 160 pixels

Pixel size: 100 microns

#m/z bins: 116,152

Contributors: Louie, K. B.; Bowen, B. P.; Cheng, X.; Berleman, J. E.; Chakraborty, R.; Deutschbauer, A.; Arkin, A.; Northen, T. R. “Replica-extraction-transfer” nanostructure-initiator mass spectrometry imaging of acoustically printed bacteria. Anal. Chem. 2013, 85, 10856–10862.

Sample: a mouse brain: left coronal hemisphere

Instrument: AbSciex 5800

Desorption/Ionization Method: NIMS

Original File: *.img

Original Filesize: 2.2 GB

OpenMSI Filesize: 0.3 GB

Image dimensions: 122 x 120 pixels

Pixel size: 80 microns

#m/z bins: 80,339

Computed data: peak-finding, NMF

Contributors: Katherine Louie, Michael Balamotis, Ben Bowen, and Trent Northen

Sample: a mouse lung

Instrument: Thermo LTQ-Orbitrap

Desorption/Ionization Method: MALDI

Original File: *.RAW

Original Filesize: 1 GB

OpenMSI Filesize: 660 MB

Image dimensions: 132 x 149 pixels

Pixel size: 50 microns

#m/z bins: 500,000

Contributors: Fehniger, T. E.; Végvári, Á.; Rezeli, M.; Prikk, K.; Ross, P.; Dahlbäck, M.; Edula, G.; Sepper, R.; Marko-Varga, G. Direct Demonstration of Tissue Uptake of an Inhaled Drug: Proof-of-Principle Study Using Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Imaging. Anal. Chem. 2011, 83, 8329–8336.



Citing OpenMSI

Oliver Rübel, Annette Greiner, Shreyas Cholia, Katherine Louie, E. Wes Bethel, Trent R. Northen, and Benjamin P. Bowen, "OpenMSI: A High-Performance Web-Based Platform for Mass Spectrometry Imaging" Analytical Chemistry 2013 85 (21), 10354-10361, DOI: 10.1021/ac402540a. [BibTeX][Online at ACS]