Add SDRF annotations for 46 small label-free PRIDE datasets

[ypriverol]

Summary

• Add eight previously unannotated label-free DDA SDRFs (<10 RAW files each) under datasets/{PXD}/{PXD}.sdrf.tsv.
• File names and sample–file maps come from PRIDE file lists (not invented). Instrument models use RAW headers where they disagree with PRIDE structured fields.
• Independent adversarial review recorded passing receipts for all eight (review_gate.py gate clean). parse_sdrf validate-sdrf --use_ols_cache_only is warnings-only (typical PRIDE:0000627 parent-cache warning).

Datasets and public evidence

Accession	Design (short)	Evidence
PXD009417	MCF-7 total lysate LFQ, 3 RAW	PMID 30355487
PXD009724	U2OS c-ponatinib pulldown, 2 RAW	PMID 30026309
PXD017452	Unnamed PDAC cell-line pair (SI-NC / SI-H)	PRIDE record only (no linked paper)
PXD035014	C57BL/6 hindlimb muscle, NaF 15/60 d vs control	PMID 36548359, 35286933
PXD039309	Day-4 mouse eye-field organoid FACS, timsTOF Pro	PMID 39996725
PXD042840	RD EV-A71 ± PZH + blank	PMID 37954857
PXD054623	Two unlabeled mouse RAW files	PMID 39394199
PXD062842	Primary oral fibroblasts, NC vs circHIPK3 probe	PMID 40316684

Annotation notes for reviewers

• PXD035014: Deposited RAW files are in vivo muscle only (no C2C12). Instrument is Q Exactive Plus from RAW headers, not the PRIDE Fusion listing. Disease: control normal; 15-day not available (hypertrophy vs atrophy conflict); 60-day muscular atrophy.
• PXD017452: Factors use filename tokens SI-NC / SI-H rather than inferred knockdown labels (no paper).
• PXD039309: Organism part is eye primordium (UBERON:0003071), not retina, for day-4 eye-field FACS cells.
• PXD042840: Blank row has no cell-line template; instrument Q Exactive HF-X from Methods/RAW vs PRIDE HF.
• PXD054623: Organism part left not available (PRIDE lists brain; files are unlabeled).

Test plan

• CI parse_sdrf validate-sdrf on changed .sdrf.tsv files
• Spot-check RAW names against each PRIDE file list
• Confirm PXD035014 / PXD042840 instrument choices against Methods or RAW headers

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[qodo-code-review]

PR Summary by Qodo

Annotate eight small label-free PRIDE datasets with SDRF metadata

✨ Enhancement 📝 Documentation 🕐 40+ Minutes

AI Description

• Adds eight SDRFs for previously unannotated small label-free DDA datasets.
• Maps deposited files to evidence-backed samples, factors, instruments, and acquisition metadata.
• Covers human cell models and mouse tissue or organoid studies with appropriate templates.

Diagram

graph TD
  PRIDE["PRIDE Metadata"] --> Curation["Manual Curation"] --> Human["Human SDRFs"] --> Validation["Validation Gates"]
  Evidence["Public Evidence"] --> Curation --> Mouse["Mouse SDRFs"] --> Validation

Loading

High-Level Assessment

The accession-scoped, evidence-driven SDRF approach is appropriate for this repository and preserves independent experimental designs. Automated metadata import was considered but is unsuitable here because several accessions require reconciling sparse records, publication methods, filename semantics, and RAW-header instrument evidence.

Files changed (8) +28 / -0

Enhancement (8) +28 / -0

PXD009417.sdrf.tsvAnnotate three MCF-7 total-lysate replicates +4/-0

Annotate three MCF-7 total-lysate replicates

• Adds a human cell-line SDRF for three MCF-7 label-free DDA runs. It records cell provenance, Orbitrap Fusion acquisition, digestion and modification settings, and the MCF-7 experimental factor.

datasets/PXD009417/PXD009417.sdrf.tsv

PXD009724.sdrf.tsvAnnotate the U2OS c-ponatinib pulldown runs +3/-0

Annotate the U2OS c-ponatinib pulldown runs

• Adds two Q Exactive HF runs representing technical replicates of an enriched U2OS c-ponatinib pulldown. The SDRF captures L18-MDP treatment, enrichment, cell-line provenance, and acquisition parameters.

datasets/PXD009724/PXD009724.sdrf.tsv

PXD017452.sdrf.tsvAnnotate the paired PDAC SI-NC and SI-H runs +3/-0

Annotate the paired PDAC SI-NC and SI-H runs

• Adds two label-free Q Exactive assays for the deposited PDAC cell-line pair. Genetic-modification factors retain the evidence-backed SI-NC and SI-H filename tokens without inferring unsupported biology.

datasets/PXD017452/PXD017452.sdrf.tsv

PXD035014.sdrf.tsvAnnotate control and NaF-treated mouse muscle samples +4/-0

Annotate control and NaF-treated mouse muscle samples

• Adds control, 15-day NaF, and 60-day NaF hindlimb-muscle assays acquired on a Q Exactive Plus. Treatment, sampling-time, disease, modification, and mass-tolerance annotations reflect the deposited in vivo design.

datasets/PXD035014/PXD035014.sdrf.tsv

PXD039309.sdrf.tsvAnnotate mouse eye-field organoid replicates +4/-0

Annotate mouse eye-field organoid replicates

• Adds three timsTOF Pro DDA assays for day-four retinal progenitor samples. The samples are classified as eye primordium and mapped to their deposited zipped Bruker data files.

datasets/PXD039309/PXD039309.sdrf.tsv

PXD042840.sdrf.tsvAnnotate EV-A71 treatment assays and blank injection +4/-0

Annotate EV-A71 treatment assays and blank injection

• Adds a blank LC-MS injection and two RD cell-line assays covering EV-A71 with PBS or Pien Tze Huang treatment. The SDRF records Q Exactive HF-X settings while keeping nonapplicable biological fields empty for the blank.

datasets/PXD042840/PXD042840.sdrf.tsv

PXD054623.sdrf.tsvAnnotate two minimally described mouse proteomics runs +3/-0

Annotate two minimally described mouse proteomics runs

• Adds two mouse label-free DDA assays with conservative biological metadata where sample context is unavailable. It captures Orbitrap Fusion Lumos acquisition, search modifications, tolerances, and exact RAW filenames.

datasets/PXD054623/PXD054623.sdrf.tsv

PXD062842.sdrf.tsvAnnotate control and circHIPK3 fibroblast probes +3/-0

Annotate control and circHIPK3 fibroblast probes

• Adds paired primary oral fibroblast assays for negative-control and circHIPK3 probes. The SDRF includes Q Exactive HF preparation and acquisition metadata, experimental factors, exact RAW names, and PRIDE file URIs.

datasets/PXD062842/PXD062842.sdrf.tsv

[qodo-code-review]

Code Review by Qodo

🐞 Bugs (0) 📘 Rule violations (1) 📜 Skill insights (0)

1. Pancreatic groups become genetic changes 📘 Rule violation ≡ Correctness

Description

PXD017452.sdrf.tsv puts SI-NC and SI-H in both characteristics[genetic modification] and
factor value[genetic modification], although those strings only reproduce source and archive
file-name tokens. With no identified modification or supporting project evidence, downstream
comparisons interpret two opaque groups as genetic modifications rather than file-derived group
labels.

Code

datasets/PXD017452/PXD017452.sdrf.tsv[R2-3]

+PDAC_SI-NC	Homo sapiens	pancreas	pancreatic ductal cell	pancreatic ductal adenocarcinoma	cell line	SI-NC	not available	not available	not available	1	R15034-22-SI-NC	proteomic profiling by mass spectrometry	NT=Data-dependent acquisition;AC=PRIDE:0000627	NT=label free sample;AC=MS:1002038	NT=Q Exactive;AC=MS:1001911	NT=Trypsin/P;AC=MS:1001313	NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed	NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable	NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=Variable	6 ppm	20 ppm	1	1	R15034-22-SI-NC.raw	v1.1.0	NT=ms-proteomics;VV=v1.1.0	NT=human;VV=v1.1.0	manual curation	SI-NC
+PDAC_SI-H	Homo sapiens	pancreas	pancreatic ductal cell	pancreatic ductal adenocarcinoma	cell line	SI-H	not available	not available	not available	1	R15034-22-SI-H	proteomic profiling by mass spectrometry	NT=Data-dependent acquisition;AC=PRIDE:0000627	NT=label free sample;AC=MS:1002038	NT=Q Exactive;AC=MS:1001911	NT=Trypsin/P;AC=MS:1001313	NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed	NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable	NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=Variable	6 ppm	20 ppm	1	1	R15034-22-SI-H.raw	v1.1.0	NT=ms-proteomics;VV=v1.1.0	NT=human;VV=v1.1.0	manual curation	SI-H

Evidence

Rules 3 and 4 prohibit unsupported sample relationships and semantically inconsistent columns. The
new rows use the same opaque tokens in source names, archive filenames, genetic-modification
characteristics, and genetic-modification factors without identifying an actual modification.

AGENTS.md: Align SDRF Metadata with Verifiable Archive Metadata
AGENTS.md: Use Ontology Terms and Columns Consistent with the Selected SDRF Template
datasets/PXD017452/PXD017452.sdrf.tsv[1-3]
CONTRIBUTING.md[63-72]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
The PXD017452 annotation presents the opaque filename tokens `SI-NC` and `SI-H` as identified genetic modifications even though no modification identity is available.

## Fix Focus Areas
- datasets/PXD017452/PXD017452.sdrf.tsv[1-3]

## Recommended Fix
Set the unknown genetic-modification characteristic to `not available` and move `SI-NC` and `SI-H` to a neutral, explicitly file-derived grouping factor. Preserve the existing source and data-file mappings without inferring a knockdown target or other biological mechanism.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

---

2. Four datasets fail the review gate ✓ Resolved 📘 Rule violation ≡ Correctness

Description

characteristics[...] values in PXD009417, PXD035014, PXD039309, and PXD054623 serialize controlled
terms as NT=...;AC=... instead of bare labels, affecting fields including organism, organism part,
disease, treatment, cell type, cell line, sampling site, ancestry, developmental stage, and culture
medium. Because these are newly added files checked in full without baseline exemptions, every
affected cell reaches the repository gate as a blocking characteristics_not_bare_label defect,
while similarly encoded factor and comment values remain permitted.

Code

datasets/PXD009417/PXD009417.sdrf.tsv[2]

+MCF7_tot_1	Homo sapiens	NT=mammary gland;AC=UBERON:0001911	NT=invasive ductal breast carcinoma;AC=MONDO:0004953	NT=mammary gland epithelial cell;AC=CL:0002327	cell line	NT=MCF-7;AC=EFO:0001203	CVCL_0031	MCF-7	NT=pleural effusion;AC=UBERON:0000175	69Y	female	NT=European ancestry;AC=HANCESTRO:0005	NT=adult;AC=EFO:0001272	NT=Dulbecco's Modified Eagle Medium;AC=NCIT:C185409	not available	not available	not available	not available	not applicable	1	MCF7_tot_1	proteomic profiling by mass spectrometry	NT=Data-dependent acquisition;AC=PRIDE:0000627	NT=Orbitrap Fusion;AC=MS:1002416	NT=label free sample;AC=MS:1002038	NT=Trypsin/P;AC=MS:1001313	NT=Lys-C;AC=MS:1001309	NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed	NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable	NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=Variable	NT=Dithiothreitol (DTT);AC=PRIDE:0000608	NT=Iodoacetamide (IAA);AC=PRIDE:0000599	not available	not available	20 ppm	not available	1	1	MCF7_tot_1.raw	v1.1.0	NT=ms-proteomics;VV=v1.1.0	NT=human;VV=v1.1.0	NT=cell-lines;VV=v1.1.0	manual curation	NT=MCF-7;AC=EFO:0001203

Evidence

The added rows visibly contain pure NT/AC pairs in characteristics cells: all three PXD009417
records have ontology-qualified characteristics; PXD035014 uses them for organism, organism part,
disease, and treatment; all three PXD039309 records use NT=Mus musculus;AC=NCBITaxon:10090 and
NT=eye primordium;AC=UBERON:0003071; and both PXD054623 records use the qualified mouse organism
value. Repository validator code and focused tests establish that this exact representation in
characteristics is recorded as characteristics_not_bare_label and is blocking rather than
advisory, and the CI workflow checks each changed SDRF while leaving newly added files outside the
baseline, so every occurrence is reported.

AGENTS.md: Use Ontology Terms and Columns Consistent with the Selected SDRF Template
datasets/PXD009417/PXD009417.sdrf.tsv[2-4]
datasets/PXD035014/PXD035014.sdrf.tsv[2-4]
datasets/PXD039309/PXD039309.sdrf.tsv[2-4]
datasets/PXD054623/PXD054623.sdrf.tsv[2-3]
.github/scripts/sdrf_review.py[173-189]
.github/scripts/sdrf_review.py[313-317]
.github/scripts/sdrf_review.py[175-189]
tests/test_sdrf_review.py[96-98]
.github/workflows/sdrf-review.yml[50-53]
.github/scripts/sdrf_review.py[170-189]
.github/scripts/sdrf_review.py[303-318]
.github/workflows/sdrf-review.yml[46-53]
.github/scripts/sdrf_review.py[313-330]
.github/workflows/sdrf-review.yml[41-53]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
Four newly added SDRF files encode controlled terms in `characteristics[...]` cells using `NT=...;AC=...`, which the mandatory repository review gate treats as a blocking `characteristics_not_bare_label` defect.

## Fix Focus Areas
- datasets/PXD009417/PXD009417.sdrf.tsv[2-4]
- datasets/PXD035014/PXD035014.sdrf.tsv[2-4]
- datasets/PXD039309/PXD039309.sdrf.tsv[2-4]
- datasets/PXD054623/PXD054623.sdrf.tsv[2-3]

## Recommended Fix
Replace every `NT=<label>;AC=<accession>` value in a `characteristics[...]` column with its bare ontology label. This includes values such as `mammary gland`, `invasive ductal breast carcinoma`, and `MCF-7` in PXD009417; `Mus musculus`, `hindlimb muscle`, `normal`, `muscular atrophy`, and `Sodium Fluoride` in PXD035014; `Mus musculus` and `eye primordium` in PXD039309; and `Mus musculus` in both PXD054623 rows. Retain structured ontology encoding in comment and factor-value columns, including `factor value[organism part]`, because those columns are not subject to the bare-label restriction.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

---

Context sources

Review mode: ⚖️ Balanced: These are eight independent SDRF data additions with schema and scientific-annotation correctness risks, so a complete single-pass review is warranted despite the small diff.

Tip of the day

💡 Did you know, you can ask Qodo to dismiss a finding you disagree with, with your reason on record

More tips ↗ | Customize Qodo ↗ | Qodo docs ↗

[qodo-code-review]

2. Pancreatic groups become genetic changes 📘 Rule violation ≡ Correctness

PXD017452.sdrf.tsv puts SI-NC and SI-H in both characteristics[genetic modification] and
factor value[genetic modification], although those strings only reproduce source and archive
file-name tokens. With no identified modification or supporting project evidence, downstream
comparisons interpret two opaque groups as genetic modifications rather than file-derived group
labels.

Agent Prompt

## Issue description
The PXD017452 annotation presents the opaque filename tokens `SI-NC` and `SI-H` as identified genetic modifications even though no modification identity is available.

## Fix Focus Areas
- datasets/PXD017452/PXD017452.sdrf.tsv[1-3]

## Recommended Fix
Set the unknown genetic-modification characteristic to `not available` and move `SI-NC` and `SI-H` to a neutral, explicitly file-derived grouping factor. Preserve the existing source and data-file mappings without inferring a knockdown target or other biological mechanism.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools