bio-proteomics-protein-inference

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