Differential proteomic analysis of bronchoalveolar lavage fluid from lung transplant patients with and without chronic graft dysfunction

Biomarkers are urgently needed for diagnosis, prognosis and monitoring of lung transplant chronic graft dysfunction. Bronchoalveolar lavage fluid (BAL) has been used in the past as proximal fluid for biomarker discovery in various lung diseases including chronic graft dysfunction (CGD). The current study describes the proteomic analysis of BAL fluids collected from 4 asymptomatic post-transplant patients and 3 patients with symptoms of CGD. BAL proteome was fractionated by size-exclusion chromatography at protein level and reverse-phase-chromatography at peptide level followed by Orbitrap® mass spectrometry detection. Our in-depth proteomic analysis identified 531 proteins, the largest catalog of BAL proteins reported to date in the context of CGD. A total of 30 and 39 proteins detected exclusively in CGD and non-CGD samples, respectively, are potential candidates for verification phase. A new protocol was developed to enhance the sensitivity of detecting less abundant proteins in BAL. ► Developed a new protocol to enhance sensitivity of detecting less abundant proteins in BAL from lung transplant patients. ► Screened BAL fluids from 4 asymptomatic post-transplant patients & 3 patients with symptoms of CGD & identified 531 proteins. ► We identified 30 proteins exclusively in BAL-CGD samples and 39 proteins in non-CGD samples.