bio-proteomics-peptide-identification
PKU-YuanGroup/OpenAI4SPeptide-spectrum matching from MS/MS with target-decoy FDR control, framing identification confidence as a property of a ranked list (q-value/PEP) rather than…
Scores out of 100 · grade A
2026-08-22Works
40% of the score100/100
- Loads cleanly: valid frontmatter, required fields present, no dangling references.
Maintained
25% of the score100/100
- no commits in the last 12 weeks
Adopted
20% of the score35/100
- 335 stars on the source repo.
Documented
15% of the score100/100
- 2,890 words with worked examples.
- Ships 2 bundled files.
Install
npx skills add PKU-YuanGroup/OpenAI4S/bio-proteomics-peptide-identificationWhat it says it does
Peptide-spectrum matching from MS/MS with target-decoy FDR control, framing identification confidence as a property of a ranked list (q-value/PEP) rather than a raw engine score (XCorr, hyperscore, Andromeda, SpecEValue). Covers sequence-database search engines (Comet, MS-GF+, MSFragger, Sage, MaxQuant, MetaMorpheus), concatenated vs separate target-decoy competition, PEP vs q-value, the multi-level FDR cascade, open/mass-tolerant search, rescoring (Percolator, mokapot, MS2Rescore), and pyOpenMS SimpleSearchEngineAlgorithm + FalseDiscoveryRate. Use when identifying peptides from tandem mass spectra and deciding what FDR threshold to act on. Protein grouping and protein-level FDR are protein-inference; PTM site localization is ptm-analysis; DIA peptide-centric scoring is dia-analysis; intensity quant is quantification.
Also in PKU-YuanGroup/OpenAI4S
| Artifact | Score | What the check found | Type | Reach | Last commit |
|---|---|---|---|---|---|
| bio-atac-seq-allele-specific-accessibilityPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today | |
| bio-atac-seq-atac-peak-callingPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today | |
| bio-atac-seq-consensus-peaksetPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today | |
| bio-atac-seq-deep-learning-atacPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today | |
| bio-atac-seq-footprintingPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today | |
| bio-causal-genomics-effector-gene-prioritizationPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today |
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