Miniaturised interaction proteomics on a microfluidic platform with ultra-low input requirements

Cristina Furlan, René A. M. Dirks, Peter C. Thomas, Robert C. Jones, Jing Wang, Mark Lynch, Hendrik Marks () and Michiel Vermeulen ()
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Cristina Furlan: Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen
René A. M. Dirks: Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen
Peter C. Thomas: Fluidigm Corporation
Robert C. Jones: Fluidigm Corporation
Jing Wang: Fluidigm Corporation
Mark Lynch: Fluidigm Corporation
Hendrik Marks: Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen
Michiel Vermeulen: Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen

Nature Communications, 2019, vol. 10, issue 1, 1-8

Abstract: Abstract Essentially all cellular processes are orchestrated by protein-protein interactions (PPIs). In recent years, affinity purification coupled to mass spectrometry (AP-MS) has been the preferred method to identify cellular PPIs. Here we present a microfluidic-based AP-MS workflow, called on-chip AP-MS, to identify PPIs using minute amounts of input material. By using this automated platform we purify the human Cohesin, CCC and Mediator complexes from as little as 4 micrograms of input lysate, representing a 50─100-fold downscaling compared to regular microcentrifuge tube-based protocols. We show that our platform can be used to affinity purify tagged baits as well as native cellular proteins and their interaction partners. As such, our method holds great promise for future biological and clinical AP-MS applications in which sample amounts are limited.

Date: 2019
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DOI: 10.1038/s41467-019-09533-y

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