Data for manuscript, "An optimized workflow for MS-based quantitative proteomics of challenging clinical bronchoalveolar lavage fluid (BALF) samples"

Clinical BALF samples are rich in biomolecules, including proteins, and useful for molecular studies of lung health and disease.  However, MS based proteomic analysis of BALF is impeded by the dynamic range of protein abundance, and potential for interfering contaminants.  We have developed a workflow that eliminates these challenges.  By combining high abundance protein depletion, protein trapping, clean-up, and in-situ tryptic digestion, our workflow is compatible with both qualitative and quantitative MS-based proteomic analysis.  The workflow includes collection of endogenous peptides for peptidomic analysis of BALF, if desired, as well as amenability to offline semi-preparative or microscale fractionation of peptide mixtures prior to LC-MS/MS analysis, for increased depth of analysis.  We show the effectiveness of this workflow on BALF samples from COPD patients.  Overall, our workflow should allow MS-based proteomics to be applied to a wide variety of studies focused on BALF clinical samples.      

Note:  Due to the nature of some of the files, file wendt005_ostr0103_18260_20210831_BALF_FAIMS_MS2_TMT16.msf was zipped into a compressed folder before uploading.