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Please get in touch with us before sample collection to make sure that we customize the MSI protocol to suit your specific application.

Sample Considerations

The most commonly used samples for MALDI MSI are fresh frozen tissues. MALDI MSI using formalin-fixed paraffin-embedded tissues (FFPE) or tissue microarrays is possible, however, it is best suited for detection of proteins, peptides, and glycans.   

MSI is a molecular histology technique; tissues should be therefore extracted carefully to:
•    Preserve the tissue shape and morphology.
•    Avoid cuts and punctures with tweezers or scalpels. 


Small, fragile or fatty tissues (i.e., tumors or plant leaves) might need embedding to facilitate cryosectioning in the first step of the MSI workflow. Acceptable embedding media include carboxymethyl cellulose (CMC) or gelatin and should be tested for each tissue type. Please note optimal cutting temperature (OCT) medium is NOT compatible with MSI.

A variety of tissues can be examined by MALDI MSI (pixel size). (A) Rabbit testis (50 µm). (B) OVCAR 3 tumor (50 µm). (C)  Hamster kidney (100 µm). (D)  Murine brain (20 µm). (E) Tadpole rostrum (50 µm). (F) Murine lower intestine (100 µm; Swiss roll technique).

Acknowledgements: Cameron laboratory (University of Victoria), Lum laboratory (BC Cancer), Picardeau laboratory (Institut Pasteur), AmberGen (Billerica, MA), Helbing laboratory (University of Victoria) and ImmunoPrecise (Victoria, BC).

Untargeted analysis

The untargeted analysis identifies differences between defined areas of a tissue section (i.e., healthy region vs. tumor region) or between experimental groups (healthy vs. diseased tissue). Lipidomics and metabolomics MSI workflows are most often employed in untargeted data analysis

Example of untargeted analysis. Lipid-based segmentation in an OVCAR 3 tumor. Segmentation creates regions of interest with similar mass spectra profiles (shown in color) based on spatial distribution and abundance of all measured molecules.

Acknowledgements: Lum laboratory (BC Cancer).

Targeted analysis

Targeted analysis determines the spatial distribution and abundance of specific ions of interest in tissue. Examples of untargeted analysis include detecting and quantifying a drug and its metabolites or detecting proteins via antibody-based probes.

Example of targeted analysis. Detection of intact proteins in the murine brain via antibody-based probes (HiPLEX, AmberGen). Antibodies coupled to photo-cleavable mass tags bind to target proteins in tissues. Mass tags that then serve as surrogates for the target proteins during the MSI data acquisition. GFAP (light blue), GLUT1 (yellow), myelin basic protein (green), NeuN (orange), NF-L (red) and SYN-I (dark blue).

Acknowledgements: AmberGen (Billerica, MA).

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