Mass Spectrometry-Based Proteomics of Intestinal Organoids

Proteomics, the large-scale study of proteins, enables the identification, quantification, and functional characterization of proteins, revealing post-translational modifications and protein interactions that are not apparent from transcriptomic data. Human organoids, which recapitulate the structural and functional complexity of native epithelial tissues, provide powerful tools to study disease mechanisms and personalize therapies. However, their culture poses challenges for efficient protein extraction and reproducible analysis. Here, we present a proteomics workflow optimized to maximize protein recovery from Matrigel-encased organoids. Samples were processed using S-Trap microcolumns to minimize losses, followed by liquid chromatography-mass spectrometry (LC-MS) in data-independent acquisition (DIA/SWATH-MS) mode for comprehensive, untargeted quantification. Library-free computational analysis using DIA-NN, combined with differential expression analysis, enabled sensitive detection of key proteins in intestinal organoids.