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SEC-MX: an approach to systematically study the interplay between protein assembly states and phosphorylation

Author

Listed:
  • Ella Doron-Mandel

    (Columbia University)

  • Benjamin J. Bokor

    (Columbia University)

  • Yanzhe Ma

    (Columbia University)

  • Lena A. Street

    (Columbia University)

  • Lauren C. Tang

    (Columbia University)

  • Ahmed A. Abdou

    (Columbia University)

  • Neel H. Shah

    (Columbia University)

  • George Rosenberger

    (Columbia University)

  • Marko Jovanovic

    (Columbia University)

Abstract

A protein’s molecular interactions and post-translational modifications (PTMs), such as phosphorylation, can be co-dependent and reciprocally co-regulate each other. Although this interplay is central for many biological processes, a systematic method to simultaneously study assembly states and PTMs from the same sample is critically missing. Here, we introduce SEC-MX (Size Exclusion Chromatography fractions MultipleXed), a global quantitative method combining Size Exclusion Chromatography and PTM-enrichment for simultaneous characterization of PTMs and assembly states. SEC-MX enhances throughput, allows phosphopeptide enrichment, and facilitates quantitative differential comparisons between biological conditions. Conducting SEC-MX on HEK293 and HCT116 cells, we generate a proof-of-concept dataset, mapping thousands of phosphopeptides and their assembly states. Our analysis reveals intricate relationships between phosphorylation events and assembly states and generates testable hypotheses for follow-up studies. Overall, we establish SEC-MX as a valuable tool for exploring protein functions and regulation beyond abundance changes.

Suggested Citation

  • Ella Doron-Mandel & Benjamin J. Bokor & Yanzhe Ma & Lena A. Street & Lauren C. Tang & Ahmed A. Abdou & Neel H. Shah & George Rosenberger & Marko Jovanovic, 2025. "SEC-MX: an approach to systematically study the interplay between protein assembly states and phosphorylation," Nature Communications, Nature, vol. 16(1), pages 1-20, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-56303-0
    DOI: 10.1038/s41467-025-56303-0
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    References listed on IDEAS

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    1. 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.
    2. Christopher D. Go & James D. R. Knight & Archita Rajasekharan & Bhavisha Rathod & Geoffrey G. Hesketh & Kento T. Abe & Ji-Young Youn & Payman Samavarchi-Tehrani & Hui Zhang & Lucie Y. Zhu & Evelyn Pop, 2021. "A proximity-dependent biotinylation map of a human cell," Nature, Nature, vol. 595(7865), pages 120-124, July.
    3. Pierre C. Havugimana & Raghuveera Kumar Goel & Sadhna Phanse & Ahmed Youssef & Dzmitry Padhorny & Sergei Kotelnikov & Dima Kozakov & Andrew Emili, 2022. "Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    4. Xiaonan Liu & Kari Salokas & Fitsum Tamene & Yaming Jiu & Rigbe G. Weldatsadik & Tiina Öhman & Markku Varjosalo, 2018. "An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations," Nature Communications, Nature, vol. 9(1), pages 1-16, December.
    5. Isabell Bludau & Max Frank & Christian Dörig & Yujia Cai & Moritz Heusel & George Rosenberger & Paola Picotti & Ben C. Collins & Hannes Röst & Ruedi Aebersold, 2021. "Systematic detection of functional proteoform groups from bottom-up proteomic datasets," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
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