Issues

• [Scientific audit] Reject non-finite precursor m/z at the raw spectrum boundary

  janusson/MassFlow#132 · Filter by author janusson opened on Oct 26, 2026
  1

• [Experimental audit] Measure HNSW recall and resolve float32 intensity-vector boundary

  enhancement
  janusson/MassFlow#130 · Filter by author janusson opened on Oct 25, 2026

• [Scientific audit] 2026-10-25 baseline findings and prioritized evidence gates

  enhancement
  janusson/MassFlow#129 · Filter by author janusson opened on Oct 25, 2026
  1

• [Validation] Design and execute a blinded standard-mixture study for a declared use case

  enhancement
  janusson/MassFlow#128 · Filter by author janusson opened on Oct 25, 2026

• [Validation] Test acquisition transfer by polarity, adduct, collision energy, and instrument

  enhancement
  janusson/MassFlow#127 · Filter by author janusson opened on Oct 25, 2026

• [Validation] Freeze an independently adjudicated reference-standard corpus and identity ledger

  enhancement
  janusson/MassFlow#125 · Filter by author janusson opened on Oct 25, 2026

• [Validation] Empirically challenge decoy calibration and query-level confidence

  enhancement
  janusson/MassFlow#126 · Filter by author janusson opened on Oct 25, 2026

• [Scientific audit] Preserve polarity, adduct, and charge in the VF-NPL benchmark corpus

  bug
  janusson/MassFlow#124 · Filter by author janusson opened on Oct 25, 2026

• [Scientific audit] Make mzTab-M export standards-valid or remove its stable claim

  bug
  janusson/MassFlow#123 · Filter by author janusson opened on Oct 25, 2026

• [Scientific audit] Define and enforce retention-time units across ingestion, search, and export

  bug
  janusson/MassFlow#122 · Filter by author janusson opened on Oct 25, 2026
  1

• 1.0: qualify installed artifacts and gate release publication manually

  janusson/MassFlow#109 · Filter by author janusson opened on Oct 22, 2026
  1

• 1.0: reconcile core installation with transitive RDKit requirements

  janusson/MassFlow#108 · Filter by author janusson opened on Oct 22, 2026
  1

• [Benchmark audit] Verify report metrics, denominators, comparisons, and provenance

  documentationenhancement
  janusson/MassFlow#97 · Filter by author janusson opened on Oct 15, 2026
  1

• [P0 / T-003] Correct fragment m/z filtering and version processing fingerprints

  janusson/MassFlow#95 · Filter by author janusson opened on Oct 15, 2026

• [Hermes Queue] Reproduce and diagnose zero-decoy FDR behavior

  janusson/MassFlow#91 · Filter by author janusson opened on Oct 12, 2026
  1

• [Hermes Queue] Audit network PR stack and scientific merge gates

  janusson/MassFlow#90 · Filter by author janusson opened on Oct 12, 2026

• R-2: ms1_tolerance (0.02 Da) conflates the precursor candidacy window with the fragment tolerance

  janusson/MassFlow#82 · Filter by author janusson opened on Oct 5, 2026

• R-3: no node-quality filtering — TriageProfile is unused, so chimeric/low-SNR spectra become graph nodes

  janusson/MassFlow#81 · Filter by author janusson opened on Oct 5, 2026

• Extend MassFlow from independent MS/MS annotation into graph-based molecular analysis

  janusson/MassFlow#75 · Filter by author janusson opened on Sep 28, 2026

• [Validation] Validate Modified Cosine vs Cosine candidate noise

  janusson/MassFlow#71 · Filter by author janusson opened on Sep 14, 2026 · v0.1.5 - Scientific Validation & Ingestion

• [Validation] Evaluate 5 ppm Gate impact on library spectra

  janusson/MassFlow#70 · Filter by author janusson opened on Sep 14, 2026 · v0.1.5 - Scientific Validation & Ingestion

• [Validation] Debug fdr_uncalibrated results & zero decoy hits

  bug
  janusson/MassFlow#68 · Filter by author janusson opened on Sep 14, 2026 · v0.1.5 - Scientific Validation & Ingestion
  2

  

• [Epic 3] Profile Numba prefilter & Polars memory allocations

  janusson/MassFlow#67 · Filter by author janusson opened on Sep 14, 2026 · v0.2.0 - Baseline Performance & Instrumentation
  

• [Epic 2] Benchmark storage backends & multi-core scaling

  janusson/MassFlow#66 · Filter by author janusson opened on Sep 14, 2026 · v0.2.0 - Baseline Performance & Instrumentation
  

• [Epic 2] Run regression & experimental benchmarks

  janusson/MassFlow#65 · Filter by author janusson opened on Sep 14, 2026 · v0.2.0 - Baseline Performance & Instrumentation