Matrix Selection for the Visualization of Small Molecules and Lipids in Brain Tumors Using Untargeted MALDI-TOF Mass Spectrometry Imaging

Matrix-assisted laser desorption/ionization mass spectrometry imaging allows for the study of metabolic activity in the tumor microenvironment of brain cancers. The detectable metabolites within these tumors are contingent upon the choice of matrix, deposition technique, and polarity setting. In this study, we compared the performance of three different matrices, two deposition techniques, and the use of positive and negative polarity in two different brain cancer types and across two species. Optimal combinations were confirmed by a comparative analysis of lipid and small-molecule abundance by using liquid chromatography-mass spectrometry and RNA sequencing to assess differential metabolites and enzymes between normal and tumor regions. Our findings indicate that in the tumor-bearing brain, the recrystallized a-cyano-4-hydroxycinnamic acid matrix with positive polarity offered superior performance for both detected metabolites and consistency with other techniques. Beyond these implications for brain cancer, our work establishes a workflow to identify optimal matrices for spatial metabolomics studies. Overall design: The extracted normal brain and tumor region were ground in liquid nitrogen, and the RNA was extracted by using the RNeasy RNA extraction kit (Qiagen 74104, Qiagen, Germantown, MD, USA) and then analyzed by using a 2200 Tapestation Analyzer (Agilent, Santa Clara, CA, USA). An input of 500 ng of RNA was used to generate libraries (TruSeq RNA Library Prep v2, Illumina, San Diego, CA, USA). Sequencing was performed on the NextSeq System (Illumina) to produce 132bp single-end reads.