Journal Article

A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease

Bhuming, Dechen, Mehta, Subina, Do, Katherine, Johnson, James E., Wagner, Reid, Rajczewski, Andrew T., Skubitz, Amy P. N., Jagtap, Pratik D., Griffin, Timothy J.

2024

Overview

Clinical metaproteomics has immense potential to offer functional insights into the microbiome and its contributions to human disease. However, there are numerous challenges in the metaproteomic analysis of clinical samples, including handling of very large protein sequence databases for sensitive and accurate peptide and protein identification from mass spectrometry data, as well as taxonomic and functional annotation of quantified peptides and proteins to enable interpretation of results. To address these challenges, we have developed a novel clinical metaproteomics workflow that provides customized bioinformatic identification, verification, quantification, and taxonomic and functional annotation. This bioinformatic workflow is implemented in the Galaxy ecosystem and has been used to characterize diverse clinical sample types, such as nasopharyngeal swabs and bronchoalveolar lavage fluid. Here, we demonstrate its effectiveness and availability for use by the research community via analysis of residual fluid from cervical swabs.

• Publisher: American Society for Microbiology
• Subject: Alveoli / Amino acid sequence / Bacterial Proteins - genetics / Bioinformatics / Bronchoalveolar Lavage Fluid - chemistry / Bronchoalveolar Lavage Fluid - microbiology / Bronchus / clinical analysis / Computational Biology - methods / Datasets / Disease / Enzymes / Host Microbial Interactions / Humans / Lavage / Mass Spectrometry / Mass spectroscopy / metaproteomics / microbiome / Microbiomes / Microbiota - genetics / Microorganisms / Pathogenesis and Host Response / Peptides / Proteins / Proteomics - methods / Resource Report / Scientific imaging / Statistical analysis / Taxonomy / Workflow