Version Compatibility

Reference examples tested with: MSnbase 2.28+, numpy 1.26+, 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.

Protein Quantification

"Quantify proteins from my mass spec data" → Extract protein abundances from MS data using label-free (LFQ, spectral counting), isobaric labeling (TMT, iTRAQ), or metabolic labeling (SILAC) approaches.

• R: MSstats::dataProcess() for feature-to-protein summarization
• Python: pandas for MaxLFQ-style normalization and ratio calculation
• R: MSnbase for isobaric tag reporter ion extraction

Label-Free Quantification (LFQ)