An R package for stable-isotope CN labeling analysis of LC–MS metabolomics data. TRACE identifies carbon–nitrogen labeling patterns in multi-isotope experiments, builds feature networks (CN labels, adducts, isotopes, fragments), assigns metabolite seeds, and annotates features against a compound database. It is a refactored R implementation of the PAVE-style workflow, built on top of MSdev objects and xcms peak tables.
See Get started for the analysis workflow and The TRACE article for a short introduction to the published study.
Publication
TRACE accompanies:
Li et al. (2026). TRACE: An Integrated Isotope-Tracing Framework for Metabolite Validation and Nutrient Fate Mapping. Analytical Chemistry. doi:10.1021/acs.analchem.6c02292
| Version | Use | Install |
|---|---|---|
1.1.0+ (main, default) |
Latest features | devtools::install_github("DrRuiLi/TRACE") |
1.0.0 (v1.0.0 / release/1.0.0) |
Reproduce the published article | devtools::install_github("DrRuiLi/TRACE", ref = "v1.0.0") |
Use tag v1.0.0 (branch release/1.0.0) for the article-published snapshot. The default main branch is TRACE 1.1.0 and includes development features added after submission.
Installation
Install MSdev and its dependencies first, then install TRACE from source.
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(c("xcms", "MSCC"))
install.packages(c("data.table", "openxlsx", "dplyr", "ggplot2", "igraph",
"BiocParallel", "patchwork", "ggrastr", "tidyr", "devtools"))
devtools::install_github("DrRuiLi/MSdev")
# Latest TRACE (1.1.0+)
devtools::install_github("DrRuiLi/TRACE")
# Published article version (1.0.0)
devtools::install_github("DrRuiLi/TRACE", ref = "v1.0.0")