Add SDRF annotations for 19 heart-tissue proteomics datasets

[enriquea]

Add SDRF annotations for 19 heart-tissue proteomics datasets

A coherent batch of cardiac annotations: human heart tissue across coronary/ischaemic,
congenital, valvular, cardiomyopathy and heart-failure phenotypes, plus four animal
cardiac-disease models. 916 sample rows, all passing parse_sdrf validate-sdrf.

Datasets

Accession	Rows	Disease focus	Organism part	Acquisition
PXD011349	56	Dilated cardiomyopathy, LV vs RV	LV + RV myocardium	DDA
PXD015497	8	Aortic stenosis, reverse remodelling	LV myocardium	DDA
PXD015498	8	Aortic stenosis, phosphoproteome	LV myocardium	DDA
PXD021990	21	Pediatric congenital aortic valve stenosis / AVI / normal	Aortic valve	DDA
PXD025002	89	Aortic valve degeneration (88 patients)	Aortic valve	DDA
PXD025096	27	Ischaemic mitral regurgitation	Mitral valve	DDA
PXD026582	16	Murine HFpEF (HFD + L-NAME)	Heart (mouse)	DDA
PXD031617	20	Murine pressure overload vs sham	Heart (mouse)	DDA
PXD039662	38	Aortic valve disease	LV myocardium	DIA
PXD045677	175	HFpEF, subcellular fractions	RV septum	DIA
PXD050610	25	Cardiac ageing (young vs old)	Heart	DIA
PXD051201	54	Aortic valve stenosis (50 valves)	Aortic valve	DIA
PXD052878	106	Diabetic ischaemic cardiomyopathy (5 groups)	LV myocardium	DIA
PXD060431	30	HFpEF vs HFrEF vs donor control	RV septum	DDA
PXD064045	20	Murine Chchd10 S55L mitochondrial cardiomyopathy	Heart (mouse)	DIA
PXD064057	30	Chchd10 S55L, solubility fractions	Heart (mouse)	DIA
PXD070758	38	Calcific aortic valve stenosis	Aortic valve	DIA
PXD073246	57	CAVD degradomics / collagen PTMs	Aortic valve	DDA
PXD079292	98	Hypertrophic cardiomyopathy	Septal myectomy	DIA

Templates: ms-proteomics v1.1.0 + human v1.1.0 (or vertebrates v1.1.0 for the
animal models), with clinical-metadata v1.0.0 and dia-acquisition v1.1.0 where used.

Validation

parse_sdrf validate-sdrf --sdrf_file datasets/<ACC>/<ACC>.sdrf.tsv --use_ols_cache_only

• 19/19 pass with sdrf-pipelines built from GitHub main (0.1.6), run on these exact paths.
• No invented file names. Every comment[data file] value was cross-checked against the
  live PRIDE file list (/projects/{acc}/files/all); 916/916 rows match a deposited run.
• Ontology terms resolved through OLS4 before use, never from memory. This mattered:
  an exact search for coronary artery disease in MONDO returns a susceptibility locus
  rather than the disorder, and PRIDE's DIA term is PRIDE:0000450.
• Rows equal deposited runs in every dataset. Two exceptions are deliberate: PXD011349 and
  PXD025096 deposit .mzXML/.mzML conversions alongside the .raw files, and only the
  .raw acquisitions are annotated.

Sample-metadata provenance

Per-sample assignments come from the deposited run names and, where available, from
open-access supplementary tables:

• PXD021990 — Supplemental Table S5 of PMC8105334
  lists every valve by SKU, tissue type (Normal / pCAVS / AVI) and age. The 20 SKUs flagged for
  proteomics match the 20 donors in the run names exactly (DB17 is marked not-included and has
  no raw file). Ages are annotated per donor.
• PXD060431 and PXD045677 — both belong to
  PMC12132713. DatasetS1 (DDA) is keyed on the
  exact IDs used in PXD060431's run names, and DatasetS13 (DIA) on the biopsy IDs embedded in
  PXD045677's run names, giving per-patient age, sex and ancestry. Note that "HFpEF" inside the
  PXD045677 mzML names is the study name, not the group — group comes from the biopsy-ID
  lookup, which is how the five non-failing DIA controls are correctly identified.

Where a grouping variable was not recoverable it was left out rather than guessed, and each
case is documented in the file header notes:

• PXD025002 — every subject had aortic valve replacement for valve degeneration, so
  aortic valve disorder is assigned to all rows; the bicuspid/tricuspid split is not in the
  file names.
• PXD039662 — whole cohort had aortic valve surgery; the stenosis/regurgitation split is not recoverable.
• PXD051201 — the paper's central variable is patient sex, which the file names do not encode, so
  characteristics[sex] is not available.
• PXD045677 — biopsies 1060, 1110 and 1705 are absent from DatasetS13; those rows carry
  not available for disease rather than an inferred group.

Points for reviewer confirmation

1. PXD025096 — CMV* in the run names is read as control mitral valve, based on the exact
   20 + 7 = 27 split matching the stated n=27 and the diseased-vs-control design. Worth a check
   against the source publication.
2. Instrument conflicts between PRIDE's declared field and the submitter's own protocol text.
   The explicit protocol statement was used and the conflict noted in each file's header:
   PXD039662 (PRIDE "Q Exactive HF" vs protocol "Exploris 480") and PXD079292 (PRIDE
   "Q Exactive HF" vs protocol "timsTOF HT" with DIA-NN).
3. PXD060431 acquisition mode. The study ran both DDA and DIA arms; the 10/10/10 file layout
   matches the DDA arm most closely and DDA is annotated, but the run names do not state the mode.
4. PXD015497/PXD015498 carry Phospho (S/T/Y) as a variable modification on both the proteome
   and phosphoproteome accessions, because the submitter's data-processing protocol declares it for
   both. Annotated as declared rather than second-guessed.

Annotation method

Produced with sdrf-skills (agent-assisted), then
validated with sdrf-pipelines. Candidate selection swept 1,379 PRIDE cardiac projects and
excluded datasets that fail the "heart tissue" criterion on inspection — iPSC-CM cultures,
plasma/serum cohorts, epicardial adipose tissue and pericardial fluid — as well as TMT
experiments deposited without a channel-to-sample key.

Two data-quality observations for the maintainers, unrelated to these files:

• PXD041192 is registered in PRIDE as
  Homo sapiens, but its data-processing protocol searches a mouse database and the description
  says "murine heart". Excluded here for that reason.
• python -m tools check in sdrf-skills reports valid accessions as hallucinated — it flags
  NT=Homo sapiens;AC=NCBITaxon:9606 while the same repo's python -m tools verify NCBITaxon:9606
  resolves it correctly.

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Important

Review skipped

Review was skipped due to path filters

⛔ Files ignored due to path filters (19)

• datasets/PXD011349/PXD011349.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD015497/PXD015497.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD015498/PXD015498.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD021990/PXD021990.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD025002/PXD025002.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD025096/PXD025096.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD026582/PXD026582.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD031617/PXD031617.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD039662/PXD039662.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD045677/PXD045677.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD050610/PXD050610.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD051201/PXD051201.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD052878/PXD052878.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD060431/PXD060431.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD064045/PXD064045.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD064057/PXD064057.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD070758/PXD070758.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD073246/PXD073246.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD079292/PXD079292.sdrf.tsv is excluded by !**/*.tsv

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