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Protein expression patterns in thin tissue sections can be determined rapidly and with high sensitivity using MALDI mass spectrometry. Depending on the type of information desired and the questions asked, this process can be divided into two modes: tissue profiling and tissue imaging.

These analyses can be thought of as two variations of the same analytical approach. Both involve sectioning a frozen piece of tissue (for example a human breast needle biopsy or a mouse brain) on a cryostat and mounting the resulting thin tissue sections on a MALDI target plate. MALDI matrix must be added to the tissue sections in order to extract and ionize the proteins of interest, and the tissue sections are analyzed with a MALDI mass spectrometer. In both cases, mass spectra are generated which represent the expression patterns of proteins in the tissue. The differences are in the scale of the experiment and the way the data are analyzed and presented.

Tissue Profiling typically involves many samples of several types, and the goal is often to discover patterns in the protein profiles of the samples that can classify the samples based on biological state (e.g., tumor vs. normal) and that can predict biological outcomes (e.g., the prognosis of a patient).

MALDI matrix is deposited on the tissue sections in discreet droplets, and each droplet is analyzed. The spectra from each spot on each section are then subjected to biostatistical analyses, where groups are compared to each other and statistical significance is assessed. Class-prediction models can be used to classify tissue types and further probe prognostic capabilities.

Tissue Imaging is usually performed on a small number of samples where the goal is to obtain a relatively high resolution image showing the distribution of various proteins in the tissue section. In this case, MALDI matrix is uniformly deposited over the entire tissue section and mass spectra are acquired in a raster or grid pattern over the tissue surface.

The intensity of any signal in the mass spectra can then be plotted as a function of position on the tissue surface. The resulting 2-dimensional ion density plots, or images, give visual representations of protein distributions.