HigH-ratiO partiaL proteolysiS with carriER proteome (HOLSER) Enables Global Structure Profiling and Site-resolved Elucidation of Ligand-Protein Interactions

ABSTRACT: Understanding how cellular proteins interact with their environment, including endogenous and exogeneous molecules, is critical for elucidating mechanisms of cellular regulation and drug action. Partial proteolysis-based techniques offer peptide-level resolution of ligand-induced conformational changes but are limited by modest proteome coverage and depth, as well as sensitivity to the experimental conditions. To overcome these limitations, we developed higH ratiO partiaL proteolysiS with carriER proteome (HOLSER), an efficient workflow that features extended digestion time for low peptide yield variability and tandem mass tag (TMT)-based multiplexing that includes full digests for enhanced proteome depth and sequence coverage as well as higher precision of abundance measurements. We demonstrate HOLSER capabilities across diverse usage cases, including global proteome structure profiling, kinase target mapping, and structural mapping of the FKBP-mTOR complex in response to rapamycin. HOLSER reveals domain-specific stabilization and identifies peptides in direct contact with ligands, providing a powerful and scalable platform for simultaneous probing structural changes at the scale of the whole proteome, individual protein domains and specific binding sites.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Hela Cell

SUBMITTER: Massimiliano Gaetani  

LAB HEAD: Massimiliano Gaetani

PROVIDER: PXD069119 | Pride | 2026-06-08

REPOSITORIES: pride