MAPLE: A Microbiome Analysis Pipeline Enabling Optimal Peptide Search and Comparative Taxonomic and Functional...

Area of Science:

• Microbiology
• Proteomics
• Bioinformatics

Background:

• Metaproteomics via mass spectrometry (MS) offers direct, quantitative insights into the functional composition of complex biological and ecological samples, particularly the human gastrointestinal microbiota.
• The human gut microbiota significantly impacts physiology and health, with metaproteomics revealing novel links to various diseases.
• Traditional MS-based proteomics requires genome data for database searching, posing challenges for metaproteomics due to the analysis of numerous species simultaneously.

Purpose of the Study:

• To develop a user-friendly pipeline for microbiome analysis (MAPLE) that overcomes database search and interpretation challenges in metaproteomics.
• To enable the definition of an optimal search space by inferring sample-specific proteomes using the principle of parsimony.
• To implement automated peptide-centric enrichment analysis for improved taxonomic and functional comparisons of microbiota.

Main Methods:

• Development of the Microbiome Analysis Pipeline (MAPLE), a user-friendly software tool.
• Inferring sample-specific proteomes based on the principle of parsimony to define an optimal search space.
• Implementation of an automated peptide-centric enrichment analysis function.

Main Results:

• MAPLE provides highly comparable or superior peptide identification rates compared to sample-specific metagenome-guided searches.
• The pipeline facilitates straightforward and comprehensive comparisons of taxonomic and functional microbiota composition.
• MAPLE addresses limitations of traditional protein-centric comparisons through automated peptide-centric enrichment analysis.

Conclusions:

• MAPLE is an effective tool for analyzing complex metaproteomic data, overcoming significant database search and interpretation challenges.
• The pipeline enhances the ability to study the functional makeup of microbiomes and their associations with health and disease.
• MAPLE offers improved and more comprehensive comparative analyses of microbial communities.