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

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

Clinical 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...

Full description

Saved in:
Bibliographic Details
Published in:Clinical proteomics Vol. 20; no. 1; p. 14
Main Authors: Weise, Danielle O, Kruk, Monica E, Higgins, LeeAnn, Markowski, Todd W, Jagtap, Pratik D, Mehta, Subina, Mickelson, Alan, Parker, Laurie L, Wendt, Christine H, Griffin, Timothy J
Format: Journal Article
Language:English
Published: England BioMed Central Ltd 02-04-2023
BioMed Central
Subjects:
Alveoli
Bronchus
Chronic obstructive pulmonary disease
Contaminants
Extracellular vesicles
Fractionation
Lavage
Lung cancer
Lung diseases
Lung diseases, Obstructive
Mass spectrometry
Mass spectroscopy
Medical research
Medicine, Experimental
Metabolites
Methodology
Patients
Peptides
Proteins
Proteomics
Sample preparation
Scientific equipment and supplies industry
Scientific imaging
Surfactants
Tryptic peptides
United States
Massachusetts
Lung disease
Bronchoalveolar lavage fluid
Quantitative proteomics
Sample preparation
Mass spectrometry
BALF
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Clinical 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. We 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. Overall, 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.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:1542-6416
1559-0275
DOI:10.1186/s12014-023-09404-1