Mass spectrometry imaging (MSI) has gained importance since the last 15 years. Matrix-assisted laser desorption/ionization (MALDI) MSI was firstly described in 1994 by Spengler [1] and by the group of Caprioli in 1997 for the localization of peptides and proteins on tissue surface [2, 3]. Since these first demonstrations, the technique was hardly improved in terms of robustness, sensitivity, spatial resolution, and data analysis. Nevertheless, the identification of the peptide/protein peaks in the m/z range between 1,500 and 25,000 remains highly challenging and requires either unsensitive top-down approaches [4] or extraction/digestion/separation steps [5]. In parallel, MALDI MSI was also used for the localization of lipid [6, 7] and primary metabolite [8] ion species in the m/z range between 250 and 1,500. In fact lipids are major constituents of cells and partially reflect the tissue state. Moreover, due to the development of instruments, such as time of flight (TOF) [9] or Orbitrap™ [10], exact mass measurements can be performed directly on tissue sections. MS/MS capabilities of most of the mass spectrometers dedicated to MSI allow the rapid structural identification of the lipid species without requiring extraction or separation.

In this chapter sample preparation for MALDI MSI of lipids [11, 12] and primary metabolites [8] on rat brain sections is described in positive and negative ion modes. In fact rat brain can be considered as a good model sample due to its high availability, its easy sample preparation, and its lipid composition depending on the different anatomical areas. Moreover, lithium cationization of the lipid species leads to better structural characterization in the positive ion mode [13]. For matrix deposition, several automated technologies are commercially available. Most of them are based on the nebulization of the matrix solution on the tissue section using a robot and allow reproducible sample preparation. Because of its ease of use and robustness, the methods presented here were developed using the TM-Sprayer™ from HTX-Imaging.