Version Compatibility

Reference examples tested with: pyOpenMS 3.1+

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.

Protein Inference

"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

The Protein Inference Problem