BALF proteomics - In-depth proteomic analysis of human bronchoalveolar lavage fluid towards the biomarker discovery for lung cancers

Lung cancer is one of the most common cancers and the leading cause of cancer-related mortality. Because the early diagnosis of the cancer is one of the major goals in lung cancer research, the molecule-based sensitive detection of biomarkers from bronchoalveolar lavage fluid (BALF) to diagnose the lung cancer has been suggested as a promising method. BALF is a fluid that can be easily obtained from patients with lung diseases and the process of collecting the fluid is relatively cheap and non-invasive. Here, we developed a novel method for in-depth single proteomic analysis of BALF by using antibody-based depletion of high abundant proteins from BALF. We identified, in total, 4,615 protein groups mapped to 4,535 gene names using LC-MS/MS. We found our method outperformed conventional methods. With the comprehensive result, we believe that this method would facilitate lung cancer biomarker discovery.