Abstract
BackgroundStable isotope tracing has become an invaluable tool for probing the metabolism of biological systems. However, data analysis and visualization from metabolic tracing studies often involve multiple software packages and lack pathway architecture. A deep understanding of the metabolic contexts from such datasets is required for biological interpretation. Currently, there is no single software package that allows researchers to analyze and integrate stable isotope tracing data into annotated or custom-built metabolic networks.ResultsWe built a standalone web-based software, Escher-Trace, for analyzing tracing data and communicating results. Escher-Trace allows users to upload baseline corrected mass spectrometer (MS) tracing data and correct for natural isotope abundance, generate publication quality graphs of metabolite labeling, and present data in the context of annotated metabolic pathways. Here we provide a detailed walk-through of how to incorporate and visualize 13C metabolic tracing data into the Escher-Trace platform.ConclusionsEscher-Trace is an open-source software for analysis and interpretation of stable isotope tracing data and is available at https://escher-trace.github.io/.
Highlights
Stable isotope tracing has become an invaluable tool for probing the metabolism of biological systems
Stable isotope tracing studies are an effective method for investigating intracellular metabolic fluxes [5, 6] that have been increasingly used in the last decade
We will walk through how a user might identify reprogramming induced by hypoxia and generate a figure that communicates this phenotype with Escher-Trace
Summary
We built a standalone web-based software, Escher-Trace, for analyzing tracing data and communicating results. Escher-Trace allows users to upload baseline corrected mass spectrometer (MS) tracing data and correct for natural isotope abundance, generate publication quality graphs of metabolite labeling, and present data in the context of annotated metabolic pathways. We provide a detailed walk-through of how to incorporate and visualize 13C metabolic tracing data into the Escher-Trace platform
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