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Changelog

See the canonical CHANGELOG.md.

v0.1.0 (2026-10-07)

First public release candidate.

  • Harmonize — eight format adapters (MaxQuant peptides/msms, DIA-NN, mzIdentML, FragPipe, pGlyco3/GlyPep-Quant glycopeptide, Spectronaut, Progenesis) behind a declarative StudyConfig/cohort YAML; 44-column canonical evidence schema with confidence tiers A–D.
  • Map — snapshot-pinned UniProtKB resolution (chunked cache, dated snapshot, offline mode), contaminant rules, exact-substring tiered mapping with no silent drops.
  • Compute — Bjellqvist pI (Biopython), alternative HH pK tables (Rodwell/EMBOSS lineage, Lehninger), MW, net charge at pH 7.4, GRAVY.
  • Background — Keil tryptic digestion (7–60 aa, configurable missed cleavages) over parent proteins.
  • Stitch — single-linkage detected-region inference, gap 25 aa, terminal-inclusive flags, ANL-020 confidence gating.
  • Bias — RQ1 digestion-matched per-protein permutation null (B=2000, seed-aware) and RQ2 per-study Woolf OR meta-analysis (FE + DerSimonian–Laird RE + I² + leave-one-out envelope), BH q-values.
  • CLI — harmonize/map/compute/background/stitch/bias/run/benchmark with the paper's parameters as defaults; offline engine benchmark.
  • Parity — harmonizer and bias models reproduce the paper's frozen artifacts exactly (70,020-row evidence table across ten studies; FE OR 0.4519 [0.4431, 0.4608]; RQ1 T = −0.6712, p = 0.0005).
  • Walkthrough — new-dataset end-to-end notebook (Sadeghi FragPipe PSMs) running fully offline on committed sample data.