Disease-specific biomarkers of pathogenic HRAS variants in human immortalized keratinocytes.
Part of the results reproduced; minor but material deviations remained.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
- Nothing in this column.
- 🔴Could not use the authors’ exact input data
- 🔴Reported values were only indirectly comparable
- 🟡A deviation arose in the data or preprocessing
- 🔴A deviation was attributed to the published material
- 🟡Reported values were not (fully) derivable from the shared data
- 🟡The deviation was non-trivial in magnitude
- 🟡The central claim did not (fully) hold under reproduction
- 🟡Overall, the reproduction showed a material discrepancy
This paper has a computational component, but its primary data is legally or ethically access-restricted — identifiable patient cohorts, rare-disease genomes, or controlled-access biobanks that cannot be openly shared. The reproduction therefore could not be attempted. That is a neutral verdict: it does not mean the result is wrong or that the authors fell short — only that, for legitimate privacy reasons, it cannot be independently checked from public data. We deliberately do NOT assign a 0–100 score here, because a low number would wrongly read as a failed reproduction.
▸Reproduction agent’s raw note
DROP (data_restricted). In-scope pipeline results were the differential expression proteome, phosphoproteome, and AP-MS interactome per HRAS variant (WT/G12S/G13R/G12V) in HaCaT keratinocytes; pipeline per the group's 2023 sister paper = Proteome Discoverer v2.4 + Sequest, FDR<0.01, P<0.05 & FC>1.5. Exhaustive control-plane search found NO publicly obtainable reproducible input: no PRIDE/ProteomeXchange/MassIVE/jPOST deposit for this paper or its 2023 sister paper (EBI Search, multiple author/system keywords), no Europe PMC text-mined accession (only Altmetric), no open preprint, and the data-availability statement + supplementary quantification tables are behind the OUP paywall (no PMCID). No analysis code repository (commercial closed-source software). Did NOT attempt: paywalled full-text purchase, contacting authors, or hijacking the desktop's mid-OAuth browser; VPN is centrally managed and off-limits. Upgrade path documented in AUDIT.md: if the supplementary per-protein/per-phosphosite abundance matrix is provided via UKE access, the differential-abundance calling step is reproducible on «our HPC». Honesty guard: no N or grade fabricated; unknowns left null.
These records describe the outcome of reproduction attempts carried out autonomously by brainbox using large language models (LLMs). They are not peer review, not an audit, and not a determination of error or misconduct by any author. A verdict reflects what one attempt could or could not reproduce — which may depend on data access, undocumented parameters, the computing environment, or the depth of effort — and not a judgement of the people who did the work. We can be wrong, and we correct mistakes quickly: every record carries a “report an error” button.
Assessment versions
Every reproduction run is kept as an immutable version — anchored to the data as it stood, with a tamper-evident chain hash. A rerun (e.g. after an author updates a deposit) adds a new version; the previous one stays on record.
-
v1 current initial assessmentassessed: 2026-06-19 ⛓ 67443f408a37
✎ I am an author of this paper
Updated or fixed a deposit, or is there an erratum? Ask us to re-run the metrics. We verify by email first; the new result is published as a new version with full history — nothing is overwritten.
Provenance — full disclosure
When this reproduction was carried out, which methodology version was used, and by whom — so the record can be audited and checked independently.
- Reproduced
- 2026-06-22
- Rubric version
- v1.0
- Assessed by
-
🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-19no human curator yet
- Last updated
- 2026-08-05
Provisional, curator- or AI-assessed, and independently checkable. A reproduction outcome states what one attempt could reproduce — not a judgement of the authors.
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — pmid-42262227
Title: Disease-specific biomarkers of pathogenic HRAS variants in human immortalized keratinocytes. Authors: Mair T, Nauth T, Voß H, Rickassel V, Deden S, Schlüter H, Rosenberger G. Journal: Human Molecular Genetics 35(11), 2026-06-09. DOI 10.1093/hmg/ddag050. PMID 42262227. PMCID: none (not in PMC; paywalled, OUP).
What the paper does (from abstract)
Immortalized human keratinocytes (HaCaT) stably expressing pathogenic HRAS variants p.G12S (Costello syndrome), p.G13R (mosaic RASopathy), p.G12V (oncogenic), vs WT. Mass-spectrometry-based interactome (AP-MS of HA-HRAS), phosphoproteome, and proteome (expression), plus immunoblotting and functional assays (proliferation, adhesion, migration). Reports variant-specific molecular consequences; p.G13R said to induce the most substantial alterations.
In-scope (pipeline-derived computational results) — IF data obtainable
- S1. Differential proteome (expression) per variant vs WT: significant up/down proteins (counts, identities, fold-changes). Pipeline: MS quant + differential stats (group precedent: Proteome Discoverer/Sequest, then p<0.05 & |FC|>1.5).
- S2. Differential phosphoproteome per variant vs WT: significant phosphosites.
- S3. Interactome (AP-MS) per variant: significant HRAS interactors vs control.
- S4. Any enrichment / PCA / clustering derived from the above tables.
Out-of-scope (wet-lab / manual — not attempted)
- Immunoblotting / western blots.
- Cell proliferation, adhesion, migration assays.
- Cell-line generation, transfections.
Pipeline / code
- No analysis code repository found (enrichment null; no GitHub/GitLab/Zenodo link; no code link in PubMed/EuropePMC). Group's 2023 sister paper (Nauth et al., HMG ddac188, PMID 35981076) processed AP-MS with Proteome Discoverer v2.4 + Sequest (commercial Thermo software), thresholds p<0.05 & FC>1.5, 885 proteins quantified → 82 significant. Same experimental system. Under P16, a third-party open tool (FragPipe/DIA-NN + MSstats/limma) on the paper's deposited data would be an equally valid reproduction — IF the data exist.
Data — BLOCKER under investigation
- Data availability statement is paywalled (only abstract is open).
- Exhaustive PRIDE/ProteomeXchange keyword search (HRAS, keratinocyte, HaCaT, Costello, RASopathy, RIN1, integrin, Nauth, Mair, Rosenberger, Voß/Schlüter, G12V/G13R) returned NO matching public deposit — neither for this 2026 paper nor for the 2023 sister paper (same group, same HaCaT/HRAS AP-MS system).
- Europe PMC text-mined accessions: none (only an Altmetric link).
- Implication: cannot yet confirm a public, obtainable dataset → reproduction feasibility hinges on (a) reading the data-availability statement and/or (b) freely-downloadable supplementary quantification tables.
CONCLUSION (2026-06-22) — DROP: data_restricted
Re-investigated exhaustively this pass. No public proteomics deposit exists for this
paper OR its 2023 sister paper (EBI Search across PRIDE/ProteomeXchange, Europe PMC
text-mining, preprint search — all negative). The data-availability statement and the
supplementary quantification tables are behind the OUP paywall; no analysis code repo
(commercial Proteome Discoverer + Sequest). The reproducible inputs are therefore not
publicly obtainable → controlled drop_reason = data_restricted. This is a determined
outcome (healthy=true), not a preliminary stub. Upgrade path: if the supplementary
per-protein/per-phosphosite abundance matrix is provided (e.g. via UKE institutional
access), the differential-abundance calling step (P<0.05 & FC>1.5) becomes reproducible
on «our HPC».
No individual results have been recorded for this entry yet.
Assessments & scoring basis
Each contributor’s verdict, the per-question basis, and the auditable, itemised worksheet behind it.
An automated assessment. It can flag an open question for review but can never, on its own, record a discrepancy verdict (C5) against a paper.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
This study was dropped as data_unavailable: the mass-spec proteomics data behind the reported biomarker results is not deposited in any public proteomics repository under any relevant keyword, and the paper plus its data-availability statement are paywalled, with no code repo. The blocker is data accessibility on the authors'/journal side (q1/q2 red, q4 red), not a measured numerical deviation or fabrication. Because nothing could be compared 1:1, derivability and the core claim are untestable rather than refuted (q5/q7 yellow), so overall this is a blocked reproduction, not a substantive discrepancy.
Automated reproduction checks whether a published result can be regenerated from the paper’s described methods and shared data. When something does not reproduce, that is not a claim of error or misconduct — most often it reflects under-described methods, software or environment differences, or gaps in data access, and some of the pre-print papers in the queue may carry issues their authors had no part in. The goal is shared awareness that rigorous, fully-described methods help everyone — never a judgement of any author.
Are you an author? We would genuinely like to hear from you — to clarify the record, add data or code, re-run the pipeline after an accession update, and publish your response right next to the assessment. Everything here is open and auditable.
🚩 Report an error in this record
Spotted something wrong — a verdict you’d contest, a data or value error, or a private detail that slipped through? Tell us, with a short justification. Authors and readers are equally welcome to write in; we review every report.
Prefer email, or the form below not working? Contact us at support@doesitreproduce.com.
Reproduction footprint
claude-opus-4-8Measured resources invested to assess this paper — sanitised (machine class only, no job ids/paths). Compute = HPC accounting (SLURM); tokens = the AI agent's session.