ArticleClinical proteomics2023
An optimized workflow for MS-based quantitative proteomics of challenging clinical bronchoalveolar lavage fluid (BALF) samples.
Article in Clinical proteomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 20 citations in OpenAlex.
- Integrated multiomics reveals a clinically relevant CXCL8-centric protein network in pediatric postinfectious bronchiolitis obliterans.Respiratory research · 2026Article
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- Synergism between Distribution, Mechanistic and Omics Analyses in Studies on Assessing Environmental Exposure and Human Health Impact.Environment & health (Washington, D.C.) · 2026Article
- Standardized sample preparation of paediatric bronchoalveolar lavage fluid for mass spectrometry based proteomic analysis.Molecular and cellular pediatrics · 2025Article
- Easy Proteomics Sample Preparation: Technical Repeatability and Workflow Optimization Across 8 Biological Matrices in a New Core Facility Setting.Proteomics · 2025Article
- The lung proteome in HIV-associated obstructive lung disease.ERJ open research · 2025Article
- Proteomic characteristics of bronchoalveolar lavage fluid in children with mild and severeFrontiers in microbiology · 2025Article
- Novel approach to exploring protease activity and targets in HIV-associated obstructive lung disease using combined proteomic-peptidomic analysis.Respiratory research · 2024Article
- Article
- Novel Approach to Exploring Protease Activity and Targets in HIV-associated Obstructive Lung Disease using Combined Proteomic-Peptidomic Analysis.Research square · 2024Article
- The MBO2/FAP58 heterodimer stabilizes assembly of inner arm dyneinMolecular biology of the cell · 2024Article
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundClinical bronchoalveolar lavage fluid (BALF) samples are rich in biomolecules, including proteins, and useful for molecular studies of lung health and disease. However, mass spectrometry (MS)-based proteomic analysis of BALF is challenged by the dynamic range of protein abundance, and potential for interfering contaminants. A robust, MS-based proteomics compatible sample preparation workflow for BALF samples, including those of small and large volume, would be useful for many researchers.
resultsWe have developed a workflow that combines high abundance protein depletion, protein trapping, clean-up, and in-situ tryptic digestion, that is compatible with either qualitative or quantitative MS-based proteomic analysis. The workflow includes a value-added collection of endogenous peptides for peptidomic analysis of BALF samples, if desired, as well as amenability to offline semi-preparative or microscale fractionation of complex peptide mixtures prior to LC-MS/MS analysis, for increased depth of analysis. We demonstrate the effectiveness of this workflow on BALF samples collected from COPD patients, including for smaller sample volumes of 1-5 mL that are commonly available from the clinic. We also demonstrate the repeatability of the workflow as an indicator of its utility for quantitative proteomic studies.
conclusionsOverall, our described workflow consistently provided high quality proteins and tryptic peptides for MS analysis. It should enable researchers to apply MS-based proteomics to a wide-variety of studies focused on BALF clinical specimens.
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