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

Ella Doron-Mandel (), Benjamin J. Bokor, Yanzhe Ma, Lena A. Street, Lauren C. Tang, Ahmed A. Abdou, Neel H. Shah, George Rosenberger and Marko Jovanovic ()
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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

Nature Communications, 2025, vol. 16, issue 1, 1-20

Abstract: 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.

Date: 2025
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DOI: 10.1038/s41467-025-56303-0

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