Version Compatibility

Reference examples tested with: pyOpenMS 3.1+, pandas 2.2+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

The pyOpenMS protein-inference class names have varied across releases. Confirm the exact spelling at the installed version with help(pyopenms.EpifanyAlgorithm) and help(pyopenms.BasicProteinInferenceAlgorithm) before relying on the reference code.

Protein Inference -- A Chosen Explanation of Peptide Evidence, Reported as Groups

"Tell me which proteins are present from my identified peptides" -> Assign the observed peptides to a minimal or probability-weighted set of proteins, reported as groups of indistinguishable proteins with a leading accession -- because bottom-up MS measures peptides, and the protein set behind them is inferred, not observed.

• Python: pyopenms.BasicProteinInferenceAlgorithm().run(peptide_ids, protein_ids) for parsimony grouping
• Python: pyopenms.EpifanyAlgorithm (TOPP tool Epifany) for Bayesian belief-propagation inference
• CLI: ProteinProphet (TPP) for EM-based probabilistic inference; Philosopher filter for FragPipe FDR