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bio-proteomics-protein-inference
Maintainer FreedomIntelligence · Last updated April 1, 2026
Protein grouping and inference from peptide identifications. Use when resolving protein ambiguity from shared peptides. Handles protein groups and protein-level FDR control using parsimony and probabilistic approaches.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-proteomics-protein-inference
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Python: pyopenms.ProteinInference() for parsimony-based grouping.
- R: Bioconductor protein inference workflows.
- Resolve protein groups from my peptide identifications" → Group peptide-spectrum matches into protein groups, resolving shared-peptide ambiguity using parsimony or probabilistic methods, then apply protein-level FDR. Python: pyopenms.ProteinInference() for parsimony-based grouping R: Bioconductor protein inference workflows.
- peptide_to_proteins = { 'PEPTIDEK': ['P12345', 'P67890'], # Shared between paralogs 'UNIQUER': ['P12345'], # Unique to P12345 'ANOTHERONE': ['P12345'], # Unique to P12345 'SHAREDK': ['P67890', 'P11111'], # Shared }.
Source Doc
Excerpt From SKILL.md
The Protein Inference Problem
Peptides can map to multiple proteins (shared peptides), making protein identification ambiguous.
## Parsimony Principle
**Goal:** Resolve protein identification ambiguity from shared peptides by finding the minimal protein set explaining all observed peptides.
**Approach:** Build a peptide-to-protein mapping, then greedily select proteins that cover the most unassigned peptides until all peptides are accounted for, producing a minimal explanatory protein list.
## pyOpenMS Protein Inference
```python
from pyopenms import ProteinIdentification, PeptideIdentification
from pyopenms import BasicProteinInferenceAlgorithm
Use cases
- Use when resolving protein ambiguity from shared peptides.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- peptide-identification - Input for protein inference
- quantification - Quantify inferred proteins
- database-access/uniprot-access - Protein annotations
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