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Mapping protein states and interactions across the tree of life with co-fractionation mass spectrometry

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  • Michael A. Skinnider

    (University of British Columbia
    Princeton University
    Princeton University)

  • Mopelola O. Akinlaja

    (University of British Columbia
    University of British Columbia)

  • Leonard J. Foster

    (University of British Columbia
    University of British Columbia)

Abstract

We present CFdb, a harmonized resource of interaction proteomics data from 411 co-fractionation mass spectrometry (CF-MS) datasets spanning 21,703 fractions. Meta-analysis of this resource charts protein abundance, phosphorylation, and interactions throughout the tree of life, including a reference map of the human interactome. We show how large-scale CF-MS data can enhance analyses of individual CF-MS datasets, and exemplify this strategy by mapping the honey bee interactome.

Suggested Citation

  • Michael A. Skinnider & Mopelola O. Akinlaja & Leonard J. Foster, 2023. "Mapping protein states and interactions across the tree of life with co-fractionation mass spectrometry," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-44139-5
    DOI: 10.1038/s41467-023-44139-5
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    References listed on IDEAS

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    1. Ronghui Lou & Weizhen Liu & Rongjie Li & Shanshan Li & Xuming He & Wenqing Shui, 2021. "DeepPhospho accelerates DIA phosphoproteome profiling through in silico library generation," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    2. Stephen Oliver, 2000. "Guilt-by-association goes global," Nature, Nature, vol. 403(6770), pages 601-602, February.
    3. Christian von Mering & Roland Krause & Berend Snel & Michael Cornell & Stephen G. Oliver & Stanley Fields & Peer Bork, 2002. "Comparative assessment of large-scale data sets of protein–protein interactions," Nature, Nature, vol. 417(6887), pages 399-403, May.
    4. Aikaterini Geladaki & Nina Kočevar Britovšek & Lisa M. Breckels & Tom S. Smith & Owen L. Vennard & Claire M. Mulvey & Oliver M. Crook & Laurent Gatto & Kathryn S. Lilley, 2019. "Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics," Nature Communications, Nature, vol. 10(1), pages 1-15, December.
    5. Edward L. Huttlin & Raphael J. Bruckner & Joao A. Paulo & Joe R. Cannon & Lily Ting & Kurt Baltier & Greg Colby & Fana Gebreab & Melanie P. Gygi & Hannah Parzen & John Szpyt & Stanley Tam & Gabriela Z, 2017. "Architecture of the human interactome defines protein communities and disease networks," Nature, Nature, vol. 545(7655), pages 505-509, May.
    6. Katja Luck & Dae-Kyum Kim & Luke Lambourne & Kerstin Spirohn & Bridget E. Begg & Wenting Bian & Ruth Brignall & Tiziana Cafarelli & Francisco J. Campos-Laborie & Benoit Charloteaux & Dongsic Choi & At, 2020. "A reference map of the human binary protein interactome," Nature, Nature, vol. 580(7803), pages 402-408, April.
    7. Cuihong Wan & Blake Borgeson & Sadhna Phanse & Fan Tu & Kevin Drew & Greg Clark & Xuejian Xiong & Olga Kagan & Julian Kwan & Alexandr Bezginov & Kyle Chessman & Swati Pal & Graham Cromar & Ophelia Pap, 2015. "Panorama of ancient metazoan macromolecular complexes," Nature, Nature, vol. 525(7569), pages 339-344, September.
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