Thoracic aortic diseases: Identification of diagnostic biomarkers using proteomic analysis
Provisional — an automated or curator check raised a specific concern and points reviewers here. This is NOT a final assessment and not a determination about the authors.
The main result did not reproduce in this reproduction attempt. Where our recomputation produced values that differ from the published ones, those discrepancies are listed below. This is a single automated attempt — not peer review and not a finding of error or misconduct — and differences can also arise from data access, undocumented parameters or the computing environment. The verdict can be contested via “report an error”.
- 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
A 0–100 reproducibility-quality score from the per-question grades, shown as a z-score: standard deviations above (+) or below (−) the mean of comparable assessments.
▸Reproduction agent’s raw note
PXD061606 deposits NO analysis code; reproduced via route P16 (re-analyse deposited Proteome Discoverer 3.0 .msf SQLite result DBs). PROTEIN-ID LAYER REPRODUCED for both cohorts by independent parsimony (lazy-greedy set-cover = PD Occam master proteins) + target-decoy protein-FDR on PSMs at <1% FDR: C1 plasma reported 1037 falls inside [802 (1%protein-FDR), 1416 (parsimony)] with 959 at >=2 unique peptides; C3 EV reported 1077 falls inside [714, 1414] with 2686 parsimony-master, from 323,448 PSMs/10,744 peptides over 2.55M Minora features. Exact integers not bit-reproducible because the deposit does not materialize PD's grouped/FDR protein table (UniquePeptidesCount/PeptideGroupCount all 0) — only PSMs + the full 19,796-candidate set are present. DIFFERENTIAL + CLINICAL LAYER NOT REPRODUCIBLE: C2/C4 (11/28 significant) blocked because StudyInformation.SampleGroup is NULL for all samples (TAA-vs-control key not deposited; quant matrices ARE present); C5/C6 (diameter/grade biomarkers) blocked because per-patient clinical metadata is not in the deposit. Plasma N=80 matches the paper; EV cohort holds 85 sample rows. Honest partial: ID counts reproducible & bracketed; the group/clinical analyses need authors' non-deposited metadata. Compute ran entirely in SLURM jobs on «our HPC» compute nodes (47.8GB EV .msf staged on node-local /tmp to bypass a saturated shared «infra» quota; result captured via stdout + copy loop).
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.
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v1 current initial assessment Score 23assessed: 2026-06-19 ⛓ a8b0265d6446
✎ 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
- 2026-06-23
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-20no 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-41061941
Title: Thoracic aortic diseases: Identification of diagnostic biomarkers using proteomic analysis Journal: Cardiovascular Pathology (2026). DOI 10.1016/j.carpath.2025.107785. PMID 41061941. Not open access. Note: Operator («email», "Schlein C") is a co-author.
Data availability
- PRIDE / ProteomeXchange: PXD061606 (public 2026-05-13), Homo sapiens, blood plasma.
230628_AortOmics_Plasma_TMT.msf(7.9 GB) — untargeted plasma proteome, TMT, Proteome Discoverer 3.0 SQLite result DB.230807_AG_Rosenberger_Aortomics_EVs.msf(47.8 GB) — exosome/EV proteome, label-free Minora, PD 3.0 SQLite result DB.AortOmics_PRM_Reanalysis.sky/.skyd/.skyl— Skyline PRM (targeted) project.- 246 Thermo
.rawfiles (8 batches × ~... ) — primary spectra.
- No analysis-code repository deposited. Reproduction is via the deposited PD result DBs (
.msf= SQLite) re-analysed per the paper's stated stats (P16: a third-party/standard tool on the paper's own data is equally valid).
Methods (from PRIDE protocols + abstract)
- Untargeted (plasma): PD 3.0 + Sequest. Fixed: carboxymethyl-C, TMT on K. Variable: M-ox, N-term acetyl, Q→pyroGlu. ≥6 aa, ≤6000 Da, 10 ppm, ≤2 missed cleavages. FDR<0.01 reversed-decoy. Quant = TMT reporter intensity at MS3, fractions per TMT batch together. Stats in Perseus 2.0.10.0: log2, column-median normalize, TMT-batch harmonize, Student t-test TAA vs control. Significant = p<0.05 AND fold-change>1.5.
- Exosome/EV: same search but TMT NOT fixed; quant via Minora Feature Detector (label-free). Same Perseus stats.
- Targeted PRM: Skyline 22.2.0.312, light/SIL ratio, manual peak QC.
In scope (pipeline-derived, reproducible)
| # | Reported result | Source | Pipeline |
|---|---|---|---|
| C1 | Untargeted analysis identified 1,037 proteins | Abstract/Results | PD3.0 protein table in plasma .msf |
| C2 | 11 proteins significantly different (p<0.05 & FC>1.5), plasma | Abstract/Results | TMT quant + Perseus-equiv t-test |
| C3 | EV analysis identified 1,077 proteins | Abstract/Results | PD3.0 protein table in EV .msf |
| C4 | 28 proteins significantly different, EV | Abstract/Results | Minora quant + Perseus-equiv t-test |
Harder / conditional (attempt if sample→group + clinical metadata recoverable)
| # | Reported result | Blocker |
|---|---|---|
| C5 | 9 proteins correlate with aortic diameter (ACTN1, CRP, TGM3, KRT84, IGHG3, DPYSL2, TSPAN8, IGKV3D-11, VDAC1) with regression B + p | Needs per-patient aortic diameter (mm) + sample↔patient map; clinical metadata likely NOT in PRIDE deposit |
| C6 | 3 proteins correlate with medial-degeneration grade (IGKV3D-11, IGHG3, APOC3) | Needs histology grades per patient (clinical, likely not deposited) |
Out of scope
- Targeted PRM absolute quantification (Skyline, manual peak curation — wet-lab/manual, not a deterministic pipeline).
- Wet-lab steps (sample depletion, TMT labelling, EV isolation, histology grading).
- Clinical regression (C5/C6) unless patient metadata is recoverable from the deposit.
Reproduction route
.msf is SQLite (see kartei proteomics-msf-pd). Download both DBs to «infra» on «our HPC», open with python sqlite3, (a) count proteins at FDR<1% → C1/C3, (b) extract per-sample quant (TMT reporter / Minora area), recover TAA-vs-control grouping, run log2 + median-normalize + batch-harmonize + Student t-test, count p<0.05 & FC>1.5 → C2/C4.
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.
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.
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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.