Nature Communications (Oct 2024)

Biofunctionalized dissolvable hydrogel microbeads enable efficient characterization of native protein complexes

  • Xinyang Shao,
  • Meng Tian,
  • Junlong Yin,
  • Haifeng Duan,
  • Ye Tian,
  • Hui Wang,
  • Changsheng Xia,
  • Ziwei Wang,
  • Yanxi Zhu,
  • Yifan Wang,
  • Lingxiao Chaihu,
  • Minjie Tan,
  • Hongwei Wang,
  • Yanyi Huang,
  • Jianbin Wang,
  • Guanbo Wang

DOI
https://doi.org/10.1038/s41467-024-52948-5
Journal volume & issue
Vol. 15, no. 1
pp. 1 – 18

Abstract

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Abstract The characterization of protein complex is vital for unraveling biological mechanisms in various life processes. Despite advancements in biophysical tools, the capture of non-covalent complexes and deciphering of their biochemical composition continue to present challenges for low-input samples. Here we introduce SNAP-MS, a Stationary-phase-dissolvable Native Affinity Purification and Mass Spectrometric characterization strategy. It allows for highly efficient purification and characterization from inputs at the pico-mole level. SNAP-MS replaces traditional elution with matrix dissolving during the recovery of captured targets, enabling the use of high-affinity bait-target pairs and eliminates interstitial voids. The purified intact protein complexes are compatible with native MS, which provides structural information including stoichiometry, topology, and distribution of proteoforms, size variants and interaction states. An algorithm utilizes the bait as a charge remover and mass corrector significantly enhances the accuracy of analyzing heterogeneously glycosylated complexes. With a sample-to-data time as brief as 2 hours, SNAP-MS demonstrates considerable versatility in characterizing native complexes from biological samples, including blood samples.