EndoGenius

EndoGenius is a program produced by the Lingjun Li Lab at the University of Wisconsin-Madison for identification of neuropeptides from mass spectrometry data.

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Getting started

• User manual

Release notes

Version 1.1.4 (Released 8/20/24)

• Support for extended library of PTMs
• Capability to search DiLeu-labeled peptides

Version 1.1.0 (Released 6/25/24)

• Integration of spectral library construction for DIA analysis
• Integration of MotifQuest
• Capability for either FDR or EndoGenius score cutoffs

Key references

EndoGenius:

• Fields, L.; Vu, N. Q.; Dang, T.C.; Yen, H.; Ma, M.; Wu, W.; Gray, M.; Li, L. (2024). EndoGenius: Optimized Neuropeptide Identification from Mass Spectrometry Datasets. Journal of Proteome Research. Link
• Fields, L.; Dang, T.; Gray, M.; Protya, S. S.; Li, L. (2025). EndoGenius: Enabling comprehensive identification and quantitation of endogenous peptides. bioRxiv. Link

MotifQuest:

• Dang, T.; Fields, L.; Li, L. (2024). MotifQuest: An Automated Pipeline for Motif Database Creation to Improve Peptidomics Database Searching Programs. Link