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Spatial Molecular Imaging of the Glycome Using Mass Spectrometry
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OpenMSI Arrayed Analysis Toolkit: Analyzing Spatially Defined Samples Using Mass Spectrometry Imaging.

Markus de Raad1, Tristan de Rond2, Oliver Rübel3

  • 1Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory , 1 Cyclotron Road, Berkeley, California 94720, United States.

Analytical Chemistry
|May 4, 2017
PubMed
Summary
This summary is machine-generated.

The OpenMSI Arrayed Analysis Toolkit (OMAAT) enables efficient analysis of large mass spectrometry imaging (MSI) datasets with spatially defined samples. This software significantly speeds up high-throughput screening and metabolic activity analysis in MSI applications.

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Area of Science:

  • Biochemistry
  • Analytical Chemistry
  • Computational Biology

Background:

  • Mass spectrometry imaging (MSI) is crucial for localizing biomolecules in biological samples.
  • Analyzing large sets of spatially arrayed MSI samples is challenging due to a lack of accessible data processing tools.

Purpose of the Study:

  • To introduce the OpenMSI Arrayed Analysis Toolkit (OMAAT), a software package designed to overcome limitations in analyzing large, arrayed MSI datasets.
  • To provide an accessible and powerful tool for researchers working with spatially defined samples in MSI.

Main Methods:

  • OMAAT is a Python-based software package integrated with the OpenMSI platform for MSI data management and analysis.
  • It utilizes a web-based Jupyter notebook interface, making it accessible to users with varying programming experience.
  • The toolkit was evaluated using a high-throughput glycoside hydrolase activity screen with 384 arrayed samples.

Main Results:

  • OMAAT analysis of a 384-sample MSI dataset reduced analysis time by over 100-fold while maintaining accurate spot detection.
  • The toolkit successfully screened metabolic activities of soil particles, revealing size-dependent sugar hydrolysis patterns.
  • Demonstrated OMAAT's effectiveness for high-throughput screening and analysis of spatially defined samples.

Conclusions:

  • OMAAT is an effective and accessible toolkit for analyzing large, spatially defined MSI datasets.
  • The software significantly enhances the efficiency of high-throughput screening and metabolic activity analysis in MSI.
  • OMAAT is available on all major operating systems with source code accessible via GitHub.