De novo sequence-ambiguity benchmark
benchmark
De novo sequence-ambiguity benchmark: benchmark. Benchmark across 8 leading DL de novo peptide sequencers on three proteomics datasets, showing large overlap of correct calls between models and that post-processing…
Benchmark across 8 leading DL de novo peptide sequencers on three proteomics datasets, showing large overlap of correct calls between models and that post-processing yields only modest gains. The shared error source is limited fragment-ion coverage, a bottleneck that database search shares as well.
| Kind | benchmark |
Code
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Data
What the papers describing this method trained it on and reported its results on, as each paper states it. A version is named only where the paper names one.
Also used, purpose not recorded
- A comprehensive LFQ benchmark dataset to validate data analysis pipelines on modern day acquisition strategies in proteo (as deposited)
- A wolf in another wolf’s clothing: Post-genomic regulation dictates venom profiles of medically-important cryptic kraits (as deposited)
- Critical Assessment of Metaproteome Investigation (CAMPI): a Multi-Lab Comparison of Established Workflows (as deposited)
Paper describing it
- Limitations of de novo sequencing in resolving sequence ambiguity (2025, bioRxiv, preprint)