Escher-Trace: a web application for pathway-based visualization of stable isotope tracing data

Abstract

Background: Stable 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.

Results: 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. Here we provide a detailed walk-through of how to incorporate and visualize ¹³C metabolic tracing data into the Escher-Trace platform.

Conclusions: Escher-Trace is an open-source software for analysis and interpretation of stable isotope tracing data and is available at https://escher-trace.github.io/ .

Keywords: Escher; Metabolism; Stable isotope tracing; Visualization; Web application.

Fig. 1

Graph types available in Escher-Trace. a Mass isotopomer distribution. b Stacked mass isotopomer distribution. c Single isotopologue label. d Kinetic single isotopologue label*. e Abundance. f Stacked abundance. g Single isotopologue abundance**. h Kinetic single isotopologue abundance*. i Quantitative abundance***. j Kinetic total abundance*. k Enrichment****. l Kinetic enrichment* ****. (*) Requires time point information to be input using Analysis ➔ Enter Time Points in the Escher-Trace Menu. (**) Shown with individual data points plotted, accessed by setting Graph Attributes ➔ Plot Individual Values to ON. (***) Requires quantitative standard information to be input using Analysis ➔ Enter Quantitative Standards in the Escher-Trace Menu. (****) Requires element count of tracer of interest to be input using Data Displayed ➔ Isotopologues to Display in the Escher-Trace Menu. Note: All data used to make graphs in this figure were simulated

Fig. 2

Escher-Trace Interface. The Escher-Trace menu can be used to cycle through graphs of labeling, abundance, and enrichment, alter graph aesthetics, normalize abundances, reorganize data and data files, save the Escher-Trace workspace and more. Data is mapped to Escher metabolite nodes by BiGG ID. Graphs of unmapped metabolites are included on the left-hand side of the Escher canvas. All graphs can be right-clicked to access additional graph types for the selected metabolite as well as graph specific functions. The Escher menu and all of its functionality related to map editing and data overlay is accessible when using Escher-Trace

Fig. 3

Data Analysis. a TCA intermediates labeling from a [U-¹³C₅]glutamine tracer, generated after the initial submission of data to Escher-Trace. b TCA intermediate abundance generated by selecting Graph Type ➔ Total Abundance from the Escher-Trace menu. c Citrate abundance before and after entry of abundance normalization information via Analysis ➔ Normalize Abundance from the Escher-Trace menu. d TCA enrichment from a [U-¹³C₅]glutamine tracer, generated by selecting Analysis ➔ Compare Metabolites from the Escher-Trace menu

Fig. 4

Complete ¹³C Figure. A complete ¹³C data figure showcasing the reprogramming of glutamine catabolism in Huh7 hepatocellular carcinoma cells grown in hypoxia compared to normoxia. Carbon circle diagrams were added by selecting Data Displayed ➔ Create Carbon Diagram from the Escher-Trace menu