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

<p>Clinical BALF samples are rich in biomolecules, including proteins, and useful for molecular studies of lung health and disease.&nbsp; However, MS based proteomic analysis of BALF is impeded by the dynamic range of protein abundance, and potential for interfering contaminants.&nbsp; We have developed a workflow that eliminates these challenges.&nbsp; 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.&nbsp; 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.&nbsp; We show the effectiveness of this workflow on BALF samples from COPD patients.&nbsp; Overall, our workflow should allow MS-based proteomics to be applied to a wide variety of studies focused on BALF clinical samples.&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;</p> <p>Note:&nbsp; Due to the nature of some of the files, file&nbsp;<em>wendt005_ostr0103_18260_20210831_BALF_FAIMS_MS2_TMT16.msf, wendt005_ostr0103_18976_20230202_quantReport.msf, cmsptc_higgi022_18988_20230203_18976DW_EnF_hcdlT_1R.raw,&nbsp;cmsptc_higgi022_18988_20230203_18976DW_EnF_hcdlT_2R.raw, cmsptc_higgi022_18988_20230203_18976DW_EnF_hcdlT_3R.raw and cmsptc_higgi022_18988_20230203_18976DW_Eclipse_noFAIMS_quantReport.msf</em>&nbsp;were&nbsp;zipped into&nbsp;compressed folders before uploading.</p>