Impact of Skin Tissue Collection Method on Downstream MALDI-Imaging

Area of Science:

• Biotechnology
• Analytical Chemistry
• Pathophysiology

Background:

• Matrix-assisted laser desorption/ionization (MALDI) imaging is a powerful tool for studying disease pathophysiology, particularly in metabolomics and lipidomics.
• Researchers commonly use formalin-fixed paraffin-embedded (FFPE) and fresh frozen tissues for MALDI imaging, each with distinct advantages and disadvantages regarding storage, processing, and data quality.

Purpose of the Study:

• To directly compare the impact of FFPE and fresh frozen sample preparation methods on MALDI imaging results in murine skin.
• To analyze how tissue processing differences affect metabolite identification and distribution using MALDI mass spectrometry imaging (MSI).

Main Methods:

• Direct comparison of FFPE and fresh frozen murine skin samples using MALDI-MSI.
• Detailed pathway analysis to assess metabolite content and distribution differences between the two fixation methods.
• Evaluation of downstream fluorescent staining compatibility for both sample types.

Main Results:

• Significant differences were observed in putative metabolite content and distribution between FFPE and fresh frozen samples.
• Only a fraction of metabolites were shared between the two methods (2037 in positive ion mode, 4079 in negative ion mode).
• Both FFPE and fresh frozen tissues were amenable to downstream fluorescent staining, offering potential time and resource savings.

Conclusions:

• Tissue fixation method (FFPE vs. fresh frozen) significantly impacts MALDI-MSI results in terms of identified metabolites and their spatial distribution.
• Despite differences, both methods allow for complementary downstream analyses like fluorescent staining, valuable for clinically precious samples.
• This study provides novel insights into MALDI-MSI of skin tissue, complementing existing research in cancer tissues.