Seo Young Sim1, Yu Ri Choi1, Jun Hyung Lee1,2, Jae Min Lim1, Seung-Eun Lee3, Kwang Pyo Kim1,3, Jin Young Kim4, Seung Hyeun Lee5, Min-Sik Kim1,2,3. 1. Department of Applied Chemistry, Global Center for Pharmaceutical Ingredient Materials, Institute of Natural Science, Kyung Hee University, Yongin, 17104, Republic of Korea. 2. Department of New Biology, DGIST, Daegu, 42988, Republic of Korea. 3. Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul, 02447, Republic of Korea. 4. Biomedical Omic Research Group, Korea Basic Science Institute, Ochang, 28119, Republic of Korea. 5. Department of Internal Medicine, Kyung Hee University School of Medicine, Seoul, 02447, Republic of Korea.
Abstract
PURPOSE: Lung cancer is among the most common cancers. Bronchoalveolar lavage fluid (BALF) can be easily obtained from patients with lung cancers. The aim is to develop a novel proteomic method of the molecule-based sensitive detection of biomarkers from BALF. EXPERIMENTAL DESIGN: BALF samples are collected from segmental bronchus of 14 patients with lung cancers from Kyung Hee University Hospital. First, BALF proteome is depleted using a depletion column, and then peptides are prepared from the enriched low abundant proteins and fractionated by high pH reverse phase liquid chromatography prior to LC-MS/MS. Data are available via ProteomeXchange with identifier PXD012645. RESULTS: A novel method is developed for in-depth proteomic analysis of BALF by combining antibody-based depletion of high abundant proteins from BALF with high pH peptide fractionation. Peptides are analyzed on a high resolution Orbitrap Fusion mass spectrometer. MaxQuant search result in the identification of 4615 protein groups mapped to 4534 genes. CONCLUSIONS AND CLINICAL RELEVANCE: It is found that the method outperformed conventional BALF proteomic methods and it is believed that this method will facilitate the biomarker research for lung cancer. In addition, it is shown that BALF will be a great source of biomarkers of lung diseases.
PURPOSE:Lung cancer is among the most common cancers. Bronchoalveolar lavage fluid (BALF) can be easily obtained from patients with lung cancers. The aim is to develop a novel proteomic method of the molecule-based sensitive detection of biomarkers from BALF. EXPERIMENTAL DESIGN: BALF samples are collected from segmental bronchus of 14 patients with lung cancers from Kyung Hee University Hospital. First, BALF proteome is depleted using a depletion column, and then peptides are prepared from the enriched low abundant proteins and fractionated by high pH reverse phase liquid chromatography prior to LC-MS/MS. Data are available via ProteomeXchange with identifier PXD012645. RESULTS: A novel method is developed for in-depth proteomic analysis of BALF by combining antibody-based depletion of high abundant proteins from BALF with high pH peptide fractionation. Peptides are analyzed on a high resolution Orbitrap Fusion mass spectrometer. MaxQuant search result in the identification of 4615 protein groups mapped to 4534 genes. CONCLUSIONS AND CLINICAL RELEVANCE: It is found that the method outperformed conventional BALF proteomic methods and it is believed that this method will facilitate the biomarker research for lung cancer. In addition, it is shown that BALF will be a great source of biomarkers of lung diseases.
Authors: Dan Shao; Lan Huang; Yan Wang; Xueteng Cui; Yufei Li; Yao Wang; Qin Ma; Wei Du; Juan Cui Journal: Database (Oxford) Date: 2021-10-13 Impact factor: 3.451