Decellularization and Enzymatic Digestion Methods to Enhance ECM Protein Detection via MALDI-MS Imaging

Matrix-assisted laser desorption ionization mass spectrometry
imaging
(MALDI-MSI) has been used to generate spatial maps of lipids, metabolites,
peptides, proteins, and glycans in tissues; however, its use for mapping
extracellular matrix (ECM) protein distributions is underexplored.
ECM proteins play a major role in various pathological conditions,
and changes in their spatial distributions affect the function and
morphology of cells within tissues. ECM protein detection is challenging
because they are large, insoluble, and undergo various post-translational
modifications, such as glycosylation. We describe here decellularization
of tissue sections coupled with serial enzymatic digestions with PNGaseF
and trypsin to improve ECM protein detection in MALDI-MSI without
disrupting ECM architecture. Decellularization leads to a 3-fold increase
in the number of proteins that are measured by MALDI-MSI. We also
introduce a binary colocalization method to improve protein identification,
which increases the number of proteins that are confidently detected.
Together, these methods enhance the spatial mapping of ECM proteins
by MALDI-MSI.