Spatial Atmospheric Pressure MALDI HRMS Analysis of Histological Sections of FFPE Samples Reveals a Unique Subset of the Metabolome.

We describe a method that allows high-resolution mass spectrometry (HRMS) imaging of metabolites in tissue sections from formaldehyde-fixed, paraffin-embedded (FFPE) biobanks. This top-down variant of MS imaging expands the molecular scope of mass spectrometry histochemistry (MSHC) from peptidomics to metabolomics. The method makes the vast archives of FFPE biobanks accessible for MSHC-based biomarker discovery research of not only small endogenous peptides but also (a subset of) metabolites. FFPE biobank tissues include well-documented clinical samples representing diseases with a high medical need and often presently not clinically diagnosable and/or curable.Our protocol starts with FFPE tissue sections prepared from samples procured from biobanks. We describe how to remove paraffin and coat the section with MALDI matrix while maximally reducing analyte delocalization or washout. We detail appropriate programming of the MSHC data acquisition and illustrate a way to process MSHC data (including conversion to the generic imzML format) and browse MSHC datasets. Finally, we show options to present the data in the form of annotated MSHC images.