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Analytical Challenges in Mapping the Subcellular Metabolome and Lipidome
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DOI：10.1039/D6AN00535G.png)
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Abstract
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Mass spectrometry–based metabolomics and lipidomics are central analytical tools for characterizing cellular chemical composition. However; most workflows still rely on the simplifying assumption of homogeneous intracellular pools; which is increasingly inadequate for spatially organized eukaryotic systems. Metabolites and lipids are distributed across subcellular compartments that differ in chemical environment; turnover; and accessibility; thereby affecting both measurement and interpretation. Recent advances in subcellular and spatial metabolomics have highlighted both the potential and the limitations of organelle-resolved analysis; particularly in terms of extraction chemistry; quantification; and data interpretation. In this review; we critically examine organelle-resolved metabolomics and lipidomics from a mass spectrometry–centric perspective; treating subcellular compartmentalization as an analytical variable rather than solely a biological feature. By comparing metabolomics and lipidomics studies on subcellular compartments; we evaluate fractionation-based; affinity-based; and spatial MS strategies; and we highlight current capabilities; common artefacts; and future opportunities; including the integration of stable isotope tracing and emerging single-organelle approaches such as Nanoscale Secondary Ion Mass Spectrometry (NanoSIMS) and Direct Organelle Mass Spectrometry (DOMS).
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