Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling

Area of Science:

• Metabolomics
• Systems Biology
• Bioinformatics

Background:

• Understanding metabolic pathways and fluxes is crucial for organism adaptation to environmental factors.
• Stable isotope labeling patterns in metabolites serve as fingerprints for metabolic events and dynamics.
• A need exists for open-source software to efficiently analyze labeled metabolite mass spectra.

Purpose of the Study:

• To introduce the open-source software LS-MIDA (Least Square Mass Isotopomer Analyzer).
• To provide a tool for rapid calculation of isotope excess and isotopomer distribution from mass spectrometry data.
• To facilitate the analysis of metabolic pathways and fluxes.

Main Methods:

• LS-MIDA processes experimental mass spectrometry (MS) data.
• Input includes metabolite composition, mass-to-charge ratios (m/z) of compounds and fragments, and experimental MS intensities.
• The software employs Brauman's least square method of linear regression.

Main Results:

• LS-MIDA calculates global isotope enrichments for metabolites or fragments.
• The software determines the molar abundances of each isotopomer.
• Results are derived by comparing labeled compound enrichments to natural abundances.

Conclusions:

• LS-MIDA offers an open-source platform for analyzing labeled metabolite MS data.
• It efficiently converts MS patterns into isotopomer enrichments.
• These enrichments are foundational for both observation-driven and model-driven metabolic flux analyses.