Background Mass spectrometry imaging (MSI) is a family of acquisition techniques producing images of the distribution of molecules in a sample, without any prior tagging of the molecules. This makes it a very interesting technique for exploratory research. However, the images are difficult to analyze because the enclosed data has high dimensionality, and their content does not necessarily reflect the shape of the object of interest. Conversely, magnetic resonance imaging (MRI) scans reflect the anatomy of the tissue. MRI also provides complementary information to MSI, such as the content and distribution of water. Results We propose a new workflow to merge the information from 2D MALDI–MSI and MRI images. Our workflow can be applied to large MSI datasets in a limited amount of time. Moreover, the workflow is fully automated and based on deterministic methods which ensures the reproducibility of the results. Our methods were evaluated and compared with state-of-the-art methods. Results show that the images are combined precisely and in a time-efficient manner. Conclusion Our workflow reveals molecules which co-localize with water in biological images. It can be applied on any MSI and MRI datasets which satisfy a few conditions: same regions of the shape enclosed in the images and similar intensity distributions.

The study used mass spectrometry imaging (MSI) to map the distribution of enzymatically degraded cell wall polysaccharides in maize stems for two genotypes and at several stages of development. The context was the production of biofuels, and the overall objective was to better describe the structural determinants of recalcitrance of grasses in bioconversion. The selected genotypes showed contrasting characteristics in bioconversion assays as well as in their lignin deposition pattern. We compared the pattern of cell wall polysaccharide degradation observed by MSI following the enzymatic degradation of tissues with that of lignin deposition. Several enzymes targeting the main families of wall polysaccharides were used. In the early stages of development, cellulose and mixed-linked β-glucans appeared as the main polysaccharides degraded from the walls, while heteroxylan products were barely detected, suggesting subsequent deposition of heteroxylans in the walls. At all stages and for both genotypes, enzymatic degradation occurred preferentially in nonlignified walls for all structural families of polysaccharides studied here. However, our results showed heterogeneity in the distribution of heteroxylan products according to their chemical structure: arabinosylated products were mostly represented in the pith center, while glucuronylated products were found at the pith periphery. The conclusions of our work are in agreement with those of previous studies. The MSI approach presented here is unique and attractive for addressing the histological and biochemical aspects of biomass recalcitrance to conversion, as it allows for a simultaneous interpretation of cell wall degradation and lignification patterns at the scale of an entire stem section.