Unbiased undepleted malignant pleural effusion proteomics study

Pleural effusion (PE) occurs as a consequence of various pathologies. Malignant effusion due to lung cancer is one of the most frequent causes. Methods for accurate differentiation of malignant from benign PE cases are an unmet clinical need. Proteomics profiling of PE has shown promising results. However, mass spectrometry (MS) analysis typically involves the tedious elimination of abundant proteins before analysis, and clinical annotation of proteomics profiled cohorts is limited. In this study, PE from 97 patients was investigated by applying label-free state-of-the-art liquid chromatography-mass spectrometry (LC-MS) to find potential novel biomarkers that correlate with immunohistochemistry assessment of tumor biopsy or survival data. The data set consists of 214 LC-MS runs.