Experimental and Data Analysis Considerations for Three-Dimensional Mass Spectrometry Imaging in Biomedical Research

Abstract

Mass spectrometry imaging (MSI) enables the visualization of molecular distributions on complex surfaces. It has been extensively used in the field of biomedical research to investigate healthy and diseased tissues. Most of the MSI studies are conducted in a 2D fashion where only a single slice of the full sample volume is investigated. However, biological processes occur within a tissue volume and would ideally be investigated as a whole to gain a more comprehensive understanding of the spatial and molecular complexity of biological samples such as tissues and cells. Mass spectrometry imaging has therefore been expanded to the 3D realm whereby molecular distributions within a 3D sample can be visualized. The benefit of investigating volumetric data has led to a quick rise in the application of single-sample 3D-MSI investigations. Several experimental and data analysis aspects need to be considered to perform successful 3D-MSI studies. In this review, we discuss these aspects as well as ongoing developments that enable 3D-MSI to be routinely applied to multi-sample studies.

Advances in spatial mass spectrometry enable in-depth neuropharmacodynamics

“…Recently, the imaging of intact biomolecules using MALDI or DESI-MSI has been extended to three dimensions, enabling acquisition of spatial distributions of analytes with depth within volumes of brain tissue specimens. This is usually done by acquiring data on serial consecutive sections of a sample, then stacking and reconstructing the 2D images of each section into a 3D MSI dataset computationally [27]. For instance, 3D MALDI-MSI has been used to visualize…”

Advances in MALDI Mass Spectrometry Imaging Single Cell and Tissues

“…Data analysis considerations for 3D-MSI data analysis is very important after data normalization (Vos et al, 2021). Benchmark datasets for 3D MALDI-MSI provide high-quality 3D imaging datasets from different biological systems at several labs, which stimulates computational research in the field of computational 3D imaging MS (Oetjen et al, 2015).…”

Batch Effects in MALDI Mass Spectrometry Imaging

“…The variation of the total-ion-count (TIC, y axis) indicates the magnitude of batch effects on a date (A–D), slide (I–V), and section level (1–71) in decreasing order. Adapted from ref ( 41 ) under a Creative Commons CC BY license.…”