Fig. 1From: An optimized workflow for MS-based quantitative proteomics of challenging clinical bronchoalveolar lavage fluid (BALF) samplesKey steps of BALF processing workflow for quantitative LC–MS/MS analysis. The workflow includes value-added collection of endogenous peptides for analysis (if desired), along with immunoaffinity-based depletion of the 14 most abundant plasma proteins, as well as protein trapping for concentration, clean-up, and tryptic digestion. The resulting peptides are compatible with isobaric peptide labeling or label-free analysis by LC–MS/MSBack to article page