Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery

Pierre C. Havugimana, Raghuveera Kumar Goel, Sadhna Phanse, Ahmed Youssef, Dzmitry Padhorny, Sergei Kotelnikov, Dima Kozakov and Andrew Emili ()
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Pierre C. Havugimana: Boston University
Raghuveera Kumar Goel: Boston University
Sadhna Phanse: Boston University
Ahmed Youssef: Boston University
Dzmitry Padhorny: Stony Brook University
Sergei Kotelnikov: Stony Brook University
Dima Kozakov: Stony Brook University
Andrew Emili: Boston University

Nature Communications, 2022, vol. 13, issue 1, 1-8

Abstract: Abstract Co-fractionation/mass spectrometry (CF/MS) enables the mapping of endogenous macromolecular networks on a proteome scale, but current methods are experimentally laborious, resource intensive and afford lesser quantitative accuracy. Here, we present a technically efficient, cost-effective and reproducible multiplex CF/MS (mCF/MS) platform for measuring and comparing, simultaneously, multi-protein assemblies across different experimental samples at a rate that is up to an order of magnitude faster than previous approaches. We apply mCF/MS to map the protein interaction landscape of non-transformed mammary epithelia versus breast cancer cells in parallel, revealing large-scale differences in protein-protein interactions and the relative abundance of associated macromolecules connected with cancer-related pathways and altered cellular processes. The integration of multiplexing capability within an optimized workflow renders mCF/MS as a powerful tool for systematically exploring physical interaction networks in a comparative manner.

Date: 2022
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DOI: 10.1038/s41467-022-31809-z

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