Isoform

Isoform analyzes stable isotope-resolved metabolomics (SIRM) mass spectrometry (MS) data to extract isotopomer distributions and infer metabolic fluxes via ODE-based kinetic modeling.

Key Features:

• Mass spectrum extraction: Extracts mass spectra of metabolites directly from raw MS recordings for downstream analysis.
• Support for isotopic substrates: Processes data from biological samples incubated with artificially enriched isotopic substrates.
• Natural isotope correction: Corrects observed spectra for natural isotope abundance to refine isotopic distribution measurements.
• Kinetic ODE simulation: Simulates corrected mass spectra using kinetic models based on ordinary differential equations (ODEs).
• Mass isotopomer dynamics: Performs dynamic simulation of mass isotopomer distributions within a biochemical network.
• Flux mapping: Infers dynamic flux maps that represent rates of biochemical reactions.

Scientific Applications:

• Metabolic flux analysis: Infers metabolic fluxes from SIRM-MS data using kinetic modeling of isotopomer dynamics.
• Pathway dynamics investigation: Studies temporal behavior of biochemical networks through simulated mass isotopomer distributions.
• Interpretation of SIRM experiments: Translates raw MS recordings from labeled-substrate experiments into corrected isotopic distributions for analysis.
• Cellular reaction-rate elucidation: Provides quantitative insight into rates of biochemical reactions in living cells.

Methodology:

Computational steps explicitly include extraction of metabolite mass spectra from raw MS recordings, correction for natural isotope abundance, and simulation of corrected spectra using kinetic models based on ordinary differential equations to simulate mass isotopomer distributions and derive dynamic flux maps.