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 13 C 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/.

NaCT/SLC13A5 facilitates citrate import and metabolism under nutrient-limited conditions

“…For tracing experiments performed in hypoxia, cancer cells were acclimated to the hypoxia chamber in basal media for 24 hours prior to applying pre-hypoxified tracing media. Mole percent enrichment Article ll OPEN ACCESS (MPE) of isotopes were calculated as the percent of all atoms within the metabolite pool that are labeled, using Escher-Trace (Kumar et al, 2020):…”

Melanoma Persister Cells Are Tolerant to BRAF/MEK Inhibitors via ACOX1-Mediated Fatty Acid Oxidation

“…Peak detection and integration were performed using the Agilent MassHunter software (B.07.01). Baseline corrected tracing data are uploaded to Escher-Tracer web server (https:// escher-trace.github.io/) (Kumar et al, 2020). The molar percent enrichment (MPE) are calculated following the Escher-Tracer protocol.…”

“…This allows the quantification of the various metabolic pathways by analyzing the labeling patterns of the downstream metabolites (Jang et al, 2018). Baseline-corrected MS labeling data are analyzed based on fractions of 12 C and 13 C integrations, as well as by Escher-Trace (Kumar et al, 2020), which allowed us to quantify the molar percent enrichment (MPE) (Figures 4 and S4). When fed with media containing [U-13 C]-glucose, parental cells showed significantly higher 13 C-labeled m+3 pyruvate and lactate compared to persister cells, indicating a higher level of anaerobic glycolysis in parental cells ( Figures S4A and S4B).…”

“…Metabolite mass isotopic integration in m+2 of each metabolite is presented by comparing the fractions of relative abundance of 12 C and 13 C isotopes. The MPE is calculated with web-based Escher-Tracer tool (Kumar et al, 2020). Data shown as mean ± SD of relative abundance of carbon isotope and MPE from four independent experiments.…”

NaCT (SLC13A5) facilitates citrate import and metabolism under nutrient-limited conditions

“…Metabolite levels and mass isotopomer distributions were analyzed with an in house Matlab script which integrated the metabolite fragment ions and corrected for natural isotope abundances. Mole percent enrichment calculations were performed using Escher-Trace (Kumar et al, 2020).…”