Enhanced Spatial Proteomics and Metabolomics from a Single Tissue Section Using MALDI-MSI and LCM-microPOTS Platforms

Spatially resolved mass spectrometry (MS)-based multiomics
workflows
are becoming more utilized for revealing the complex biology that
occurs within tissues. However, these approaches commonly require
multiple independent tissue sections to analyze the metabolite and
protein compositions of these samples. This poses a significant challenge
in preserving cell- or region-specific molecular fidelity, as variations
between tissue sections can compromise the accurate correlation of
molecular data. Here, we developed workflows for comprehensive multiomics
profiling from a single tissue section (STS) using different MS modalities.
We enhanced the functionality of an electrically insulated substrate
by employing metal-assisted approaches that enabled both MS-based
untargeted spatial metabolomics and proteomics from STS. This allowed
metabolite imaging using matrix-assisted laser desorption/ionization-MS
imaging (MALDI-MSI), without compromising it for subsequent proteome
profiling with laser capture microdissection (LCM)-based technology.
Specifically, implementing copper tape as a backing for polyethylene
naphthalate (PEN) slides enabled the detection of >140 metabolites
across a poplar root tissue section using MALDI-trapped ion mobility
spectrometry time-of-flight (timsTOF)-MS. Afterward, we detected 6571
unique proteins from two distinct root regions by leveraging LCM technology
coupled to our microdroplet based sample preparation approach. We
also developed an alternative workflow utilizing gold-coated PEN substrates
for imaging with MALDI-Fourier-transform ion cyclotron resonance (FTICR)-MS,
which permitted the profiling of >170 metabolites and the identification
of 6542 unique proteins across a single poplar root tissue section.
These results were comparable to using each omics analysis independently.
These approaches offer new opportunities for high-resolution molecular
profiling of multiple omics levels across biological tissues.