정희정 (한국기초과학지원연구원)

권요셉 (한국기초과학지원연구원)

정희정 (한국기초과학지원연구원)

권요셉 (한국기초과학지원연구원)

The intestine is a challenging for quantitative LC–MS/MS-based proteomic analysis because of its high lipid content and complex architecture, and standardized workflows for whole intestinal tissue remain limited. Most previous studies have focused on specific intestinal segments, isolated fractions, or disease models rather than normal whole intestinal tissue.

In this study, we established a standardized LC–MS/MS workflow for whole intestinal tissue by incorporating a delipidation clean-up step after protein extraction. Proteomic analysis was performed on the duodenum, jejunum, ileum, colon, and rectum of normal C57BL/6 mice. Protein identification and quantification were conducted using QI for Proteomics, followed by principal component analysis, Pearson correlation analysis, differential expression analysis, and Ingenuity Pathway Analysis (IPA).

The workflow yielded reproducible, region-specific protein expression profiles across the intestinal tract. Differential expression and IPA using the colon as the reference further revealed distinct molecular characteristics, including region-specific marker proteins and enriched biological functions.

This study presents a systematic LC–MS/MS workflow incorporating a delipidation step and provides reference proteomic data for the normal mouse intestine. The workflow and dataset will serve as resources for comparative proteomic studies of intestinal disease models, host–microbiota interactions, and standardized intestinal proteomics.