Version Compatibility

Reference examples tested with: MSstats 4.10+, MSnbase 2.28+, iq 1.9+, 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 -- Reconstructing Protein Abundance from Ions Whose Physical Origin Dictates the Irreducible Error

"Quantify proteins from my mass spec data" -> Reconstruct a protein-by-sample abundance matrix from peptide/reporter ion signals, choosing a summarizer and normalizer that match where the signal physically came from -- because the measurement's physical origin sets an error that no normalization can remove.

• R: MSstats::dataProcess() (Tukey median polish summarization) for label-free feature-to-protein
• R: iq::maxLFQ() for the real MaxLFQ algorithm (delayed normalization + maximal peptide-ratio least-squares)
• R: MSnbase::quantify(reporters=TMT10) + purityCorrect() for isobaric reporter extraction
• R/Python: sample-loading + IRS scaling to bridge TMT plexes; per-sample median centering for LFQ