Tutorial of IsoPairFinder
Abstract
Understanding metabolic pathways in gut microbes is crucial for advancing microbiome research, yet identifying specific metabolic intermediates remains challenging due to the complexity of LC-MS data analysis. IsoPairFinder is a novel tool designed to streamline Stable Isotope Tracing (SIT) metabolomics from gene-edited microbes, enabling efficient identification of pathway intermediates and gene functions. IsoPairFinder offers an end-to-end workflow that: (1) Detects differential ion signals resulting from gene mutations; (2) Consolidates redundant LC-MS features (isotopes, adducts, fragments); (3) Pairs ¹²C/¹³C features to highlight candidate intermediates. Compatible with popular metabolomics data processing tools, IsoPairFinder empowers researchers to rapidly generate actionable biological insights. This tutorial provides step-by-step guidance for using IsoPairFinder.
The ways to access IsoPairFinder are listed below:
| Access Method | Type | Link | Document |
|---|---|---|---|
| R Package | Command line tools | Link | Documentation |
| Web Server | Graphic interface within GNPS2 ecosystem | Link | Documentation |
If you used IsoPairFinder in your research, please cite the following paper:
- Zhiwei Zhou, Yuanyuan Liu, Mingxun Wang, Dylan Dodd, IsoPairFinder: A Computational Workflow for Prioritizing LC–MS Feature Pairs Representing Candidate Microbial Pathway Intermediates from Stable Isotope Tracing Metabolomics, J. Am. Soc. Mass Spectrom.*, 2026, In Press Link
For questions, contact Zhiwei Zhou (Stanford University).