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. 2018 Jan;29(1):8-16.
doi: 10.1007/s13361-017-1809-6. Epub 2017 Sep 20.

MSiReader v1.0: Evolving Open-Source Mass Spectrometry Imaging Software for Targeted and Untargeted Analyses

Affiliations

MSiReader v1.0: Evolving Open-Source Mass Spectrometry Imaging Software for Targeted and Untargeted Analyses

Mark T Bokhart et al. J Am Soc Mass Spectrom. 2018 Jan.

Abstract

A major update to the mass spectrometry imaging (MSI) software MSiReader is presented, offering a multitude of newly added features critical to MSI analyses. MSiReader is a free, open-source, and vendor-neutral software written in the MATLAB platform and is capable of analyzing most common MSI data formats. A standalone version of the software, which does not require a MATLAB license, is also distributed. The newly incorporated data analysis features expand the utility of MSiReader beyond simple visualization of molecular distributions. The MSiQuantification tool allows researchers to calculate absolute concentrations from quantification MSI experiments exclusively through MSiReader software, significantly reducing data analysis time. An image overlay feature allows the incorporation of complementary imaging modalities to be displayed with the MSI data. A polarity filter has also been incorporated into the data loading step, allowing the facile analysis of polarity switching experiments without the need for data parsing prior to loading the data file into MSiReader. A quality assurance feature to generate a mass measurement accuracy (MMA) heatmap for an analyte of interest has also been added to allow for the investigation of MMA across the imaging experiment. Most importantly, as new features have been added performance has not degraded, in fact it has been dramatically improved. These new tools and the improvements to the performance in MSiReader v1.0 enable the MSI community to evaluate their data in greater depth and in less time. Graphical Abstract ᅟ.

Keywords: Data analysis; High mass resolving power; Image processing; Mass spectrometry imaging; Mass spectrometry software; Open-source; Orbitrap.

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Figures

Figure 1
Figure 1
Loading multiple imaging data sets. The images presented are for cholesterol [M+H+-H2O]+ in 12 sagittal mouse brain tissue sections.
Figure 2
Figure 2
MSiQuantification tool for absolute quantification MSI experiments. The tool allows ROIs to be drawn for an area of the tissue to be quantified (A) and up to 10 calibration spots (B). One the ROIs have been drawn, the concentration of each calibration spot can be inputted in the MSiQuantification pop-up window (C). The ion images presented are for emtricitabine [M+Na+]+ in a human cervical tissue section. The calibration curve spots of stable isotope labeled emtricitabine [M+Na+]+ were spotted directly on top of the tissue section prior to IR-MALDESI MSI.
Figure 3
Figure 3
Polarity switching and polarity filtering are implemented for the mzXML and imzML file formats as the data is loaded. In this case, healthy (left) and cancerous (right) hen ovarian tissue sections were analyzed using a polarity pattern of [+--+, odd] and only the (+) polarity scans are retained.
Figure 4
Figure 4
MSiImage tool for overlaying an optical image with the ion image of putatively assigned desmosterol (m/z 367.3363, [M+H+-H2O]+) obtained in a whole-body IR-MALDESI analysis 2-day old neonatal mouse.
Figure 5
Figure 5
Top: Screenshot of MSiReader interface showing the ion image of glutathione (m/z 306.0766, [M-H+]) in a healthy hen ovary tissue section analyzed with negative mode IR-MALDESI. The mass measurement accuracy function can be accessed by right-clicking on the image axes. Bottom: Heatmap of MMA in ppm of glutathione over the tissue region (denoted by magenta line on the ion image). Calculated MMA values for all interrogated voxels are presented in histogram form with an overlaid Gaussian fit, demonstrating normality of the MMA distribution. The dashed lines on the histogram demonstrate the ±2.5 ppm tolerance that the ion image was generated with.

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