Figure 1 Schematic representation of a typical MALDI-MSI workflow Figure 1 | Schematic representation of a typical MALDI-MSI workflow. Biopsy-obtained tissue from a rat joint is cut into thin sections and placed on a conductive plate. Potential pretreatment steps include ethanol washes, chemical derivatization and on-tissue digestion. Washing steps are usually performed in order to remove ionization-suppressing small molecules such as salts or lipids. Chemical derivatization is widely applied to enhance the ionization efficiency of specific molecules and thus improve their detection. The application of proteolytic enzymes on the tissue (on-tissue digestion) can be used to detect and identify larger proteins (1). Matrix is deposited in a uniform manner across the tissue sections (2). The resulting ions obtained after laser ionization are detected by their mass-to-charge ratio (m/z) in a mass analyser, leading to a mass spectrum that shows the intensity of each detected ion precursor. Each m/z peak in the mass spectrum corresponds to a specific peptide in a specific location of the tissue section (3). 2D images are reconstructed from mass spectra acquired from different areas of sample surface. These images show the spatial distribution and relative abundance of the detected peptides. Tissue sections might also be stained for histological analysis to correlate MSI images with histological information (4). MALDI, matrix-assisted laser desorption/ionization; MSI, mass spectrometry imaging. Rocha, B. et al. (2016) Mass spectrometry imaging: a novel technology in rheumatology Nat. Rev. Rheumatol. doi:10.1038/nrrheum.2016.184