MetaProClust-MS1: an MS1 Profiling Approach for Large-Scale Microbiome Screening.
Caitlin M A Simopoulos1,2,3, Zhibin Ning1,2,3, Leyuan Li1,2,3
1Ottawa Institute of Systems Biology, University of Ottawagrid.28046.38, Ottawa, Ontario, Canada.
Msystems
|August 11, 2022
Summary
MetaProClust-MS1 screens microbial communities and proteomes using only MS1 profiles, reducing the need for time-consuming MS/MS analysis. This computational framework prioritizes samples for further metaproteomic characterization and aids in clinical diagnostics.
Area of Science:
- Microbiology
- Proteomics
- Bioinformatics
Background:
- Metaproteomics reveals microbial community functions but acquiring data via tandem mass spectrometry (MS/MS) is resource-intensive.
- Computational methods are needed to reduce the resource requirements for metaproteomic data acquisition.
- High-throughput metaproteomic studies are increasingly common in gut microbiome research, necessitating efficient screening approaches.
Purpose of the Study:
- To introduce MetaProClust-MS1, a computational framework for microbiome feature screening.
- To prioritize samples for follow-up MS/MS analysis, reducing time and cost.
- To demonstrate the utility of MS1-only profiles for proteomic screening across various applications.
Main Methods:
- Developed MetaProClust-MS1, a computational framework utilizing MS1-only profiles for proteomic screening.
- Tested MetaProClust-MS1 on gut microbiome data from fecal samples using short (15-min) and long (60-min) chromatographic gradients.
- Reanalyzed data from a clinical study of pediatric inflammatory bowel disease and an Alzheimer's disease mouse model experiment.
Main Results:
- MetaProClust-MS1 identified robust gut microbiome responses to xenobiotics with comparable cluster topologies to MS/MS data.
- The framework distinguished between inflammatory bowel disease diagnoses (ulcerative colitis and Crohn's disease) using MS1 profiles.
- Identified proteome shifts in Alzheimer's disease mouse models after small-molecule treatment using MS1 profiles.
Conclusions:
- MetaProClust-MS1 effectively screens microbiomes and single-species proteomes using only MS1 profiles.
- The approach is potentially generalizable to any proteomics experiment, especially for large-scale screening.
- MetaProClust-MS1 offers a promising novel approach for clinical diagnostic screening and prioritizing samples for in-depth metaproteomic characterization.
