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Why Trust PTM

This page is about the current flagship ptm surface.

The trustworthy part today is the repository's ambiguity discipline around localization, targetability, and follow-up burden across two public PTM packages plus one published cross-package report. PTM is outsider-auditable in a bounded sense, not a decision-grade promotion story.

PTM is also one of the clearest examples of deeper real science in the current repository. The public packet now rests on broader localization, occupancy, motif, and follow-up surfaces, while still refusing to blur localization evidence into stronger regulatory language than the current proof supports.

Open First

  • benchmark:ptm_localization_consistency
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_localization_review_package/package_manifest.json
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_localization_review_package/evidence/localization_results.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_ambiguity_stress_review_package/package_manifest.json
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_ambiguity_stress_review_package/cross_package_generalization.json
  • packages/bijux-proteomics-core/src/bijux_proteomics/ptm/benchmarks.py
  • packages/bijux-proteomics-intelligence/src/bijux_proteomics_intelligence/reviews/benchmarks.py

Current Trust Earned

  • outsider_review:ptm is complete enough to count as an outsider-auditable flagship family.
  • benchmark evidence tier is external_reproduction_package.
  • public claim support is advisory.
  • the runtime package is now ptm-localization-review-corpus.
  • the companion family-transfer report is currently highly_stable at 0.8, but targetability confidence weakens materially on the ambiguity-stress package.
  • the recommendation posture is recommend_with_downgrade.
  • the lab posture is exploratory_only.
  • decision-grade wording remains blocked because the shared consequence chain still ends at exploratory-only follow-up and can collapse once PTM burden or ambiguity widens again.

Best Cross-Surface Audit

  • open Workflow Families first to compare PTM against the other flagship families before reading its localization support as a universal promotion story
  • open Benchmark Assets and the PTM package files above when the question is whether localization and ambiguity remain inspectable together
  • open Black-Box Benchmark Dashboard when the question becomes whether motif, occupancy, and follow-up outputs are publicly traceable through the runtime lane
  • open Workflow Recommendation Confidence and Workflow Consequence Maps when the dispute shifts from localized evidence to whether the broader PTM sentence should still stay narrow

What The Reader Is Really Auditing

  • whether localization evidence stays separated from broader occupancy or regulatory meaning
  • whether ambiguity remains a first-class public surface instead of a quiet footnote
  • whether targetability and follow-up pressure narrow the same sentence that the benchmark package seems to strengthen

Why This Packet Is Scientifically Real

  • PTM now has a public story that includes localization, ambiguity, targetability, and follow-up burden together instead of letting one stronger localization artifact dominate
  • the ambiguity-stress companion package proves the repository is willing to publish where targetability weakens
  • the product value is bounded site-localized review, not broad occupancy or regulatory authority

Exact Claims

  • PTM review preserves localization confidence, ambiguity, and PSI-MOD grounding across the pinned phospho-oriented package
  • PTM benchmark outputs separate localized evidence from broader occupancy or regulatory claims

Why This Surface Is Stronger Now

  • PTM now exposes localization, ambiguity, occupancy, motif, and follow-up surfaces as one connected public story instead of a thin benchmark-only page
  • the ambiguity-stress companion package keeps targetability weakness visible instead of letting one stronger localization packet overdefine trust
  • the surrounding recommendation and consequence pages now make it easier to see why localization support does not automatically become regulatory support

What You Can Trust Right Now

  • ambiguity remains visible
  • comparator and ambiguity limits remain visible
  • the repo does not flatten PTM excitement into promotion language
  • the tracked public package keeps localization, feature, FASTA, and raw-spectrum context tied together in one inspectable surface
  • the runtime bundle now preserves localization, occupancy, motif, and lab-targeting outputs inside one checked PTM run family
  • the companion ambiguity-stress package publishes a second family-transfer check at packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_ambiguity_stress_review_package/cross_package_generalization.json

Why The Public Sentence Still Narrows

  • occupancy and regulatory interpretation remain narrower than localization evidence
  • ambiguity still weakens targetability under the companion package
  • exploratory-only follow-up keeps the consequence chain bounded

Honest Reader Outcome

  • a reviewer should leave trusting the bounded localization story more than the older docs allowed
  • the same reviewer should still refuse broader PTM promotion language until ambiguity, targetability, and consequence closure improve together

What You Should Not Trust Yet

  • comparator drift or missing external execution parity still materially limits this public workflow claim
  • occupancy and regulatory interpretation still remain narrower than localization evidence
  • targetability confidence weakens materially on the ambiguity-stress package
  • PTM follow-up remains exploratory

Consequence Boundary

  • open Workflow Consequence Maps before widening PTM language beyond bounded localization support
  • open What Changed The Recommendation before claiming that one targetable site family changed broader PTM posture
  • open Workflow Refusal Handbook when the honest next move may still be stop, rerun, narrow, or refuse
  • one doubled assay burden or one wider ambiguity failure still demotes the public sentence faster than this page alone might suggest

Evidence Grounding