R46

Schema round. Theme: methods/ directory + type: method page-type.

Sub-file of log — see parent for index.

[2026-05-20] R46 | methods/ directory + type: method schema

User-initiated: “should we start a methods or protocols section for things like SELEX and other methods commonly used by the studies we frequently reference?” → confirmed scope (technique reference for the literature we cite, distinct from sops/ workflow guidance and experiments/ user-authored protocols). User explicitly OK with textbook-style content for validated methods even when commonly known. User to source Current Protocols volumes (Protein Science, Mouse Biology, Cell Biology, Bioinformatics, Pharmacology) as authoritative anchor for future seeding.

• added: methods/ directory; CLAUDE.md § directory map entry; CLAUDE.md § “type: method” schema block with frontmatter spec + body-structure conventions + seeding discipline; CLAUDE.md § Lint pass — type:method >24 months cadence.
• added: methods/mass-spec-age-hydrolysates.md (R46 pilot) — LC-MS/MS quantification of AGE crosslinks in acid-hydrolyzed collagen. Drafted from general field knowledge + Sell 2005 / Voziyan 2026 / Dammann 2012 / Streeter 2020 / Li 2025 method-section content visible in wiki footnotes. verified: false; flagged for full verification pass when Current Protocols anchor sourced.
• updated: processes/glucosepane.md § “What it is” — backlinks to new methods page from the canonical-quantification sentence.
• updated: index.md — new “Methods reference” Dataview block immediately after “Experiments” section.
• pilot rationale: glucosepane page’s “non-invasive measurement is lacking” caveat + AGE-quantification methodology recurs across ≥6 wiki pages (glucosepane, pentosidine, CML, AGE process page, dermis, SAF biomarker). High deduplication value. Future methods candidates surfaced during pilot:
  • methods/skin-autofluorescence-as-age-proxy.md (currently confused with the SAF biomarker page; needs separation — biomarker page = device + clinical claims; methods page = “fluorescence as non-specific AGE surrogate” caveat)
  • methods/mr-causal-inference.md (currently scattered across sops/finding-population-evidence.md + 10+ protein pages with mr-causal-evidence: frontmatter)
  • methods/pc-clock-vs-elastic-net-clock.md (R26/R43 schema escalations track architecture in frontmatter but the rationale lives in body text of ≥3 biomarker pages)
  • methods/scrna-aging-atlas-pipelines.md (Tabula Muris Senis / CellxGene Census; sops/finding-singlecell-aging.md is workflow-side; methods/ side would cover analytical caveats)
• next: pilot the seeder-driven verification pass on the mass-spec-age-hydrolysates page once Current Protocols is sourced; assess whether the methods/ pattern is worth expanding to the 3-4 candidates above.