Version Compatibility

Reference examples tested with: matchms 0.33+, SIRIUS 6.x, MetFrag 2.5+

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

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

Spectral matching needs precursor m/z on every MS/MS spectrum (add_precursor_mz filter) or ModifiedCosine silently returns zeros. Level 1 needs an authentic standard run in the same lab under the same method; no software output can substitute for it.

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

Metabolite Annotation

"Annotate my metabolomics features with compound identities" -> Map each feature's m/z and MS/MS to candidate structures, then attach an explicit confidence level to every name.

• Python: matchms.calculate_scores() for library matching (matchms)
• CLI: sirius ... formulas fingerprints structures canopus for in-silico formula/structure/class (SIRIUS)