Calis-p

Calis-p extracts stable carbon isotope fingerprints (SIFs) of individual species from metaproteomic datasets to quantify species-resolved δ13C values for studying food sources and metabolic pathways.

Key Features:

• High-throughput δ13C measurement: Calculates accurate δ13C values for individual species within microbial communities from metaproteomic data.
• Direct protein-SIF approach: Implements a direct protein-SIF method that determines SIFs directly from proteins, bypassing bulk measurements by isotope ratio mass spectrometers.
• Benchmarking and accuracy: Validated on 20 pure culture microorganisms with reproducible SIF values that align with gold-standard bulk measurements.
• Analysis of complex communities: Detects species-resolved SIFs in mock and complex microbial assemblages.
• Symbiosis metabolic insights: Applied to obligate bacteria-animal symbiosis to validate physiological hypotheses and reveal metabolic insights of symbionts.

Scientific Applications:

• Environmental microbiology: Enables species-resolved investigation of carbon sources and metabolic pathways in environmental microbiology.
• Biogeochemical cycling: Supports investigation of carbon flow and biogeochemical cycling through species-level δ13C measurements.
• Microbial interactions with plants and animals: Traces microbial interactions with plants and animals using species-resolved isotope fingerprints.
• Microbial ecology and symbiosis: Facilitates linking isotope signatures to metabolic processes in studies of microbial ecology and symbiosis.

Methodology:

Requires scored peptide-spectrum match (PSM) tables for samples and calibration materials and raw mass spectrometry data in mzML format, and applies the direct protein-SIF approach to derive species-resolved δ13C values without relying on isotope ratio mass spectrometers.