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

Ying Zhu, Kerem Can Akkaya, Julia Ruta, Nanako Yokoyama, Cong Wang, Max Ruwolt, Diogo Borges Lima, Martin Lehmann and Fan Liu ()
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Ying Zhu: Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Kerem Can Akkaya: Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Julia Ruta: Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Nanako Yokoyama: Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Cong Wang: Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Max Ruwolt: Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Diogo Borges Lima: Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Martin Lehmann: Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Fan Liu: Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)

Nature Communications, 2024, vol. 15, issue 1, 1-18

Abstract: Abstract The 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. Biochemical and imaging-based follow-up studies confirm that CLASP allows discovering mitochondria-associated proteins and revising previous protein sub-compartment localization and membrane topology data. We also validate the CLASP concept in synaptic vesicles, demonstrating its applicability to different sub-cellular compartments. This study extends the scope of cross-linking mass spectrometry beyond protein structure and interaction analysis towards spatial proteomics, and establishes a method for concomitant profiling of sub-organelle and membrane proteomes.

Date: 2024
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DOI: 10.1038/s41467-024-47569-x

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