Software and analysis code from the lab of Dr. Lingjun Li, School of Pharmacy and Department of Chemistry, UW–Madison.
The group develops mass spectrometry methods for neuropeptidomics, quantitative proteomics and glycomics, mass spectrometry imaging, ion mobility-MS, and capillary electrophoresis-MS. This organization hosts the lab's open-source tools and the code and data behind its publications.
🌐 lilabs.org · 🧰 Lab resources · 𝕏 @LiResearch · 🦋 @liresearch.bsky.social
| Tool | What it does | Papers |
|---|---|---|
| cNPDB | Comprehensive empirical crustacean neuropeptide database (web app) | bioRxiv |
| EndoGenius | Database searching optimized for neuropeptide identification from MS data | J. Proteome Res. · bioRxiv (EndoGenius v2) · bioRxiv (DIA neuropeptidomics) |
| Hybrid EndoGenius | Hybrid de novo sequencing + database searching for endogenous peptide discovery | bioRxiv |
| MotifQuest | Automated motif database creation to improve peptidomics database searching | J. Am. Soc. Mass Spectrom. |
| HyPep | Neuropeptide identification and discovery via sequence homology search | J. Proteome Res. |
| MSIght | Modular platform for confident untargeted MS imaging annotation | J. Proteome Res. |
| MSI-Parser | Analysis of single-cell MS imaging data | Nat. Commun. |
Other lab tools not hosted here (Metandem, PRESnovo) are listed on the resources page.
Most repositories accompany a publication. If you use one, please cite the associated paper linked in its README. Questions about a specific tool are best raised as an issue in that repository.