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bioRxiv · 10.1101/2022.05.05.490733

Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topology

Zhu, Y.·Akkaya, K. C.·Borges Lima, D.·Wang, C.·Lehmann, M.·Liu, F.
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Abstract

The specific functions of cellular organelles and sub-compartments depend on their protein content, which can be characterized by spatial proteomics approaches. However, many spatial proteomics methods are limited in their ability to resolve organellar sub-compartments, profile multiple sub-compartments in parallel, and/or characterize membrane-associated proteomes. Here, we develop a cross-link assisted spatial proteomics (CLASP) strategy that addresses these shortcomings. Using human mitochondria as a model system, we show that CLASP can elucidate spatial proteomes of all mitochondrial sub-compartments and provide topological insight into the mitochondrial membrane proteome in a single experiment. Biochemical and imaging-based follow-up studies demonstrate that CLASP allows discovering mitochondria-associated proteins and revising previous protein sub-compartment localization and membrane topology data. This study extends the scope of cross-linking mass spectrometry beyond protein structure and interaction analysis towards spatial proteomics, establishes a method for concomitant profiling of sub-organelle and membrane proteomes, and provides a resource for mitochondrial spatial biology.

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Zhu, Y., Akkaya, K. C., Borges Lima, D., Wang, C., Lehmann, M., Liu, F.. 2022-05-05. Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topology. https://doi.org/10.1101/2022.05.05.490733

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