Ramid

Ramid extracts and processes 12C/13C mass spectra from NetCDF mass spectrometer files to support 13C-assisted fluxomic analysis using ODE-based kinetic modeling.

Key Features:

• R implementation: Implemented in R for computational processing of stable isotope-resolved metabolomics (SIRM) data.
• Mass spectra extraction: Extracts mass spectra of targeted 12C/13C-labeled metabolites from raw mass spectrometer NetCDF files.
• SIRM workflow support: Supports stable isotope-resolved metabolomics workflows specific to 13C-assisted fluxomic studies.
• Natural isotope abundance correction: Performs correction of extracted spectra for natural isotope abundance.
• Dynamic flux mapping (ODE-based): Simulates corrected spectra using ordinary differential equation (ODE) based kinetic models to generate dynamic flux maps.

Scientific Applications:

• Flux quantification and mapping: Enables precise quantification and mapping of metabolic fluxes from 13C-labeling data.
• Systems biology and metabolomics: Facilitates integration of 13C-labeling data into systems biology and metabolomics analyses.
• Metabolic disease research: Applicable to tracing carbon flow for studies of metabolic diseases.
• Bioprocess optimization: Supports optimization of biotechnological processes by tracking distribution of 13C-labeled substrates.
• Fundamental metabolism studies: Enables investigation of cellular energy production and resource allocation using 13C tracers.

Methodology:

Implemented in R; reads NetCDF mass spectrometer files; extracts mass spectra of 12C/13C-labeled metabolites; applies natural isotope abundance correction; simulates corrected spectra with ODE-based kinetic models to generate dynamic flux maps; supports SIRM workflows.