Version Compatibility

Reference examples tested with: DIA-NN 1.9+, pandas 2.2+, pyarrow 15+

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

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

DIA Analysis -- Scoring Reconstructed Peak Groups Against a Decoy Null, Filtered at the Right q-Value Context

"Identify and quantify proteins from my DIA runs" -> Reconstruct, per candidate peptide, a set of co-eluting fragment extracted-ion chromatograms (XICs) and score whether that peak group is real against a decoy null -- because every wide-isolation-window MS2 is chimeric, so the problem is deconvolution and peak-group scoring, not spectrum matching.

• CLI: diann --fasta-search for library-free (directDIA) discovery and quantification
• CLI: diann --lib predicted.speclib for the deep-learning predicted-library route (the modern default)
• CLI: diann --lib experimental.tsv for an experimental or chromatogram library
• CLI: OpenSwathWorkflow + pyprophet when explicit run/experiment/global FDR contexts must be auditable