In the current study, we use mass spectrometry-based proteomics to analyze bronchoalveolar lavage fluid (BALF) samples collected from a cohort of 43 patients of which 30 patients present a lung function that is stable over 36 months and 13 patients that develop CLAD within the first-year post-transplant. The mass spectrometry method used label free quantification (LFQ) of all the proteins detected as well as heavy labelled peptides for absolute quantification of mucins and related proteins.