MetaProfiler

MetaProfiler performs protein stable isotope probing (protein-SIP) analysis to identify and quantify partially labeled peptides and characterize metabolic activity and protein synthesis dynamics in gut microbiome communities.

Key Features:

• Protein Stable Isotope Probing (SIP): Utilizes protein-SIP to identify and quantify partially labeled peptides derived from metabolically active microorganisms and to track protein synthesis over time.
• Local False Discovery Rate Correction: Implements algorithms for calculating local false discovery rates to improve accuracy of peptide identification.
• Comprehensive Multi-level Analyses: Performs taxonomic, functional, phylogenetic, and time-series analyses to provide multifaceted views of microbiome dynamics.
• Incorporation Profile Analysis: Analyzes incorporation profiles of labeled peptides across taxa and clusters of orthologous groups (COGs) to reveal intra- and inter-taxa variation.
• Empirical Application Example: Has been applied to stool samples from mice fed nitrogen-15–labeled hydrolysate, identifying thousands of non-redundant peptides and their heavy counterparts.

Scientific Applications:

• Microbial metabolic activity profiling: Quantifies labeled peptide incorporation to map active metabolic processes within gut microbiome communities.
• Dietary and environmental response studies: Enables comparison of community functional responses to dietary changes, environmental shifts, or interventions using labeled substrates.
• Temporal protein synthesis analysis: Provides time-series analysis of protein synthesis dynamics to study temporal aspects of microbial activity.
• Metaproteomics and microbiome research: Supports identification and interpretation of microbial interactions and functional roles at peptide and taxon levels.

Methodology:

Computational steps explicitly include protein stable isotope probing (protein-SIP) analysis, identification and quantification of partially labeled peptides, calculation of local false discovery rates, taxonomic/functional/phylogenetic/time-series analyses, and analysis of labeled-peptide incorporation profiles across taxa and clusters of orthologous groups (COGs).