Orthrus: an AI-powered, cloud-ready, and open-source hybrid approach for metaproteomics
preprint · bioRxiv · 2024
preprint · bioRxiv · 2024. Yun Chiang et al. While metaproteomics provides invaluable insight into microbial communities and functions, significant…
| Date | 2024-11-15 |
| Type | preprint |
| Venue | bioRxiv |
| Publisher | Cold Spring Harbor Laboratory |
| Contribution | downstream-application |
| DOI | 10.1101/2024.11.15.623814 |
| Citations (OpenAlex) | 5 |
Abstract
While metaproteomics provides invaluable insight into microbial communities and functions, significant bioinformatics challenges persist due to data complexity and the limitations of database searching. Orthrus is a hybrid approach combining transformer-based de novo sequencing with Casanovo and database searching with Sage plus Mokapot rescoring. Benchmarking against PEAKS 11, MaxQuant, and MetaNovo demonstrated high peptide outputs, taxonomic diversity, and proteome coverage. Orthrus is Python-based and accessible via Google Colaboratory.
Methods and tools
- Orthrus: Open-source metaproteomics pipeline combining Casanovo transformer-based de novo sequencing with Sage database search and Mokapot rescoring.
Data used
Cites (4)
- Accounting for Digestion Enzyme Bias in Casanovo (2024) crossref
- Sequence-to-sequence translation from mass spectra to peptides with a transformer model (2024) crossref
- MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets (2023) crossref
- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) crossref
Cited by (3)
- De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution (2025) both
- The proteome of the late Middle Pleistocene Harbin individual (2025) crossref
- De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution (2024) crossref