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MFA Suite™

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MFA Suite™ consists of three applications: Extracellular Timecourse Analysis (ETA),  Isotopomer Network Compartmental Analysis (INCA), and Program for Integration and Rapid Analysis of Mass Isotopomer Distributions (PIRAMID).

MFA Suite™ ETA is used to estimate specific rates (i.e., on a per-cell basis) of nutrient uptake and product excretion in cultured cells. The user provides the program with measurements of the target analyte concentrations in extracellular medium that has been exposed to cells for varying lengths of time. The user must also provide measurements of cell number or concentration over time. Based on these inputs, the program will perform regression analysis to estimate the specific growth rate of the cells and the specific uptake and excretion rates of the target analytes. The program also calculates statistical metrics of goodness-of-fit and standard errors of the estimated parameters. The ETA application is available for license free of charge as downloadable MATLAB P-code.

MFA Suite™ INCA is a MATLAB-based software package for isotopomer network modeling and metabolic flux analysis. The software can simulate both steady-state and transient isotope labeling experiments using the elementary metabolite unit (EMU) method. It can also estimate pathway fluxes based on extracellular flux measurements, pool size measurements, and/or mass isotopomer measurements supplied to the program. The software can perform a variety of statistical tests to determine goodness-of-fit, to compute parameter confidence intervals (i.e., uncertainty), and to assess model identifiability. It can also perform constraint-based analysis of metabolic networks (e.g., flux balance analysis, flux coupling analysis, etc.) and optimize the design of isotope labeling experiments using computational search algorithms. The software provides a framework for comprehensive analysis of metabolic networks using mass balances and isotopomer balances. The generation of balance equations and their computational solution is completely automated and can be performed on networks of arbitrary complexity. The graphical user interface (GUI) allows the user to input reaction information and experimental data in a simple format, while offering a variety of powerful analysis tools to design and interpret isotope labeling experiments. All INCA data objects can be loaded and manipulated from the MATLAB command line, and the driver routines can be called directly from the command line or invoked within custom MATLAB scripts. INCA also offers built-in parallelization capabilities for running certain functions within a distributed computing environment. The INCA application is available for licensing free of charge to academic users and for an annual end user license fee for non-academic customers. 
MFA Suite™ PIRAMID is a MATLAB-based tool that provides a user-friendly, graphical user interface (GUI)-driven program to automate the extraction of isotopic information from mass spectrometry (MS) data sets. This tool can simultaneously extract ion chromatograms for various metabolites from multiple data files in common vendor-agnostic file formats (.cdf, .mzml, .mzxml), locate chromatographic peaks based on a targeted list of characteristic ions and retention times, and integrate mass isotopomer distributions (MIDs) for each target ion. These MIDs can be corrected for natural isotopic background based on the user-defined molecular formula of each ion. PIRAMID offers support for datasets acquired from low- or high-resolution (HR) MS, and single (MS) or tandem (MS/MS) instruments. It also enables the analysis of single or dual labeling experiments using a variety of isotopes (i.e., 2H, 13C, 15N, 18O, 34S).