MAPLE

MAPLE performs metaproteomics analysis by mass spectrometry (MS) to profile proteins expressed across multiple organisms within complex microbiota samples.

Key Features:

• Optimal Peptide Search: Employs a principle of parsimony to infer sample-specific proteomes and refine the peptide search space, improving peptide identification accuracy relative to sample-specific metagenome-guided searches.
• Comparative Taxonomic and Functional Analysis: Implements automated peptide-centric enrichment analysis to compare taxonomic and functional composition between different microbiota samples.

Scientific Applications:

• Microbiota–disease association discovery: Enables exploration of associations between microbiota protein expression profiles and disease states by providing quantitative functional assessments.
• Functional profiling of complex environments: Supports quantitative assessment of microbial functional makeup in complex environments, including the human gastrointestinal tract, by improving peptide identification and downstream interpretation.

Methodology:

Leverages genome data to define search spaces, infers sample-specific proteomes using a principle of parsimony, and applies automated peptide-centric enrichment analysis to MS-derived peptide identifications.