Mass spectrometry imaging in the earth sciences—A tutorial to the micrometer-scale mapping of molecular fossils via MALDI FT-ICR MS

Mass spectrometry imaging (MSI) is widely used in biomedical sciences, as well as in plant sciences or microbiological studies. However, it is much less prominent in the earth sciences, despite holding enormous potential. For example, marine and lake sediments are excellent archives of the past, as they store the remnants of organisms from the water column and from surrounding land. These organisms leave behind fossil molecules that can be employed to reconstruct the environmental conditions during their lifetime, and hence to study the climate evolution of Earth. Focusing on matrix-assisted laser desorption/ionization (MALDI) imaging, we herein show that it is possible to read these molecular signatures in micrometer-sized spots, and thus to characterize climate variability with unprecedented resolution. However, obtaining this information is not trivial, and challenges arise from the nature of geological samples, low analyte concentrations, strong matrix effects, and from the need to reference the micrometer-scale maps to the original, large samples. Here we present a detailed tutorial on (i) how to select and prepare suitable samples, (ii) how to analyze them while avoiding the most common pitfalls and (iii) how to process the resulting large and complex dataset. We hope that this tutorial might contribute to inspire the use of MALDI in paleoenvironmental reconstructions in particular and in the earth sciences in general, and at the same time be useful to imaging applications across research fields.