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.

A novel method for in‐depth proteomic analysis of bronchoalveolar lavage fluid (BALF) by combining antibody‐based depletion of high abundant proteins from BALF with high pH peptide fractionation is developed. The method results in 4615 protein groups which is one of the highest number of BALF proteins identified from lung cancer patients. This is reported by Seo Young Sim, Yu Ri Choi, Jun Hyung Lee, Jae Min Lim, Seung‐Eun Lee, Kwang Pyo Kim, Jin Young Kim, Seung Hyeun Lee, and Min‐Sik Kim in article 1900028.