Add PXD016582 HLA class I ligandome SDRF (colorectal organoid clones)

[ypriverol]

Summary

• Adds datasets/PXD016582/PXD016582-immunopeptidome.sdrf.tsv: HLA class I ligandome (W6/32 IP) runs for a colorectal-cancer patient-derived organoid panel (PMID 33087703).
• Covers 5 organoid clones (T1, T3, T4, T5) plus matched normal colon organoid (N41) from one 71-year-old female CRC patient, each with 3 technical replicates on two acquisition methods (Q Exactive HF-X HCD and Orbitrap Fusion Lumos EThcD) — 30 runs total.
• File names and run counts come from the PRIDE archive's 7z-encoded headers (read via HTTP range requests, not a full download).
• HLA typing (A02:01, B15:01/57:01, C*03:04/06:02) and IP/search parameters are from the manuscript Methods; no typing method or ppm/Da search tolerance is stated in the paper, so those fields are not available.
• Proteome_Raw.7z (separate shotgun proteome experiment, same PXD) is intentionally not covered by this file.

Validation

• parse_sdrf validate-sdrf --use_ols_cache_only passes for the declared templates (ms-proteomics, human, immunopeptidomics); only the repo-wide PRIDE:0000627 parent-cache warning.
• Repo's .github/scripts/sdrf_review.py gate: 1/1 clean.

Test plan

• CI validate / review checks pass
• Spot-check RAW names against the PRIDE file list for PXD016582

[coderabbitai]

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[qodo-code-review]

PR Summary by Qodo

Add PXD016582 colorectal organoid immunopeptidome SDRF

✨ Enhancement 📝 Documentation 🕐 20-40 Minutes

AI Description

• Adds reusable SDRF metadata for 30 PXD016582 HLA class I ligandome runs.
• Maps four tumor clones and matched normal organoid across two acquisition methods.
• Records donor, HLA typing, enrichment, instrumentation, and manuscript-derived search parameters.

Diagram

graph TD
  A["Organoid panel"] --> B["W6/32 enrichment"] --> C{"Acquisition path"} --> D["HF-X HCD"] --> F["30 SDRF assays"] --> G["SDRF templates"]
  C --> E["Lumos EThcD"] --> F

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High-Level Assessment

A single run-level SDRF is the best fit because both acquisition methods cover the same biological panel and share donor, HLA, and enrichment metadata. Splitting by instrument would fragment one coherent ligandome experiment, while including the separate shotgun proteome archive would mix distinct experimental scopes.

Files changed (1) +31 / -0

Other (1) +31 / -0

PXD016582-immunopeptidome.sdrf.tsvAdd run-level metadata for the PXD016582 HLA class I ligandome +31/-0

Add run-level metadata for the PXD016582 HLA class I ligandome

• Adds 30 assay records for four colorectal cancer organoid clones and one matched normal organoid, each measured in three technical replicates by HF-X HCD and Lumos EThcD. Captures donor characteristics, HLA alleles, W6/32 enrichment, acquisition and search settings, RAW filenames, disease factors, and applicable SDRF templates.

datasets/PXD016582/PXD016582-immunopeptidome.sdrf.tsv

[qodo-code-review]

Code Review by Qodo

🐞 Bugs (0) 📘 Rule violations (0) 📎 Requirement gaps (0)

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[Copilot]

🟡 Changes recommended

Several metadata and summary corrections remain before approval.

Get a fresh assessment by requesting another Copilot review.

Pull request overview

Adds a 30-run SDRF annotation for PXD016582’s colorectal organoid HLA class I ligandome experiment.

Changes:

• Annotates tumor clones T1, T3, T4, T5 and matched normal N41.
• Captures HLA typing, enrichment, instruments, acquisition methods, and run metadata.
• Covers HCD and EThcD technical replicates.

File summaries

File	Summary
datasets/PXD016582/PXD016582-immunopeptidome.sdrf.tsv	New SDRF annotation; requires explicit organoid grouping, corrected modification metadata, distinct biological replicate assignments, and corrected summary count wording.

Review details

Suppressed comments (2)

datasets/PXD016582/PXD016582-immunopeptidome.sdrf.tsv:2

• These modification fields do not match the PXD016582 search settings. The study used fixed carbamidomethylation on C (NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed) and variable oxidation on M plus protein N-terminal acetylation (NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=Variable); this row instead declares variable cysteinylation (UNIMOD:312) and omits the acetylation entry. Update the modification columns in every row, otherwise the SDRF misrepresents the search parameters.

Patient41_T1	Homo sapiens	colon	colorectal cancer	epithelial cell of large intestine	cell	adult	71Y	female	not available	Patient41	1	MHC class I protein complex	HLA-A*02:01;HLA-B*15:01;HLA-B*57:01;HLA-C*03:04;HLA-C*06:02	not available	W6/32	immunoaffinity purification	20180507_OR16_Ag6_5607264_SA_MHC_HCD_clone1-IP1	proteomic profiling by mass spectrometry	NT=Data-dependent acquisition;AC=PRIDE:0000627	NT=Q Exactive HF-X;AC=MS:1002877	NT=label free sample;AC=MS:1002038	NT=Cysteinyl;AC=UNIMOD:312;TA=C;MT=Variable	NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable	NT=unspecific cleavage;AC=MS:1001956	NT=beam-type collision-induced dissociation;AC=MS:1000422	35% NCE	not available	not available	2	3	100m/z	10% acetic acid	400m/z-650m/z	NT=orbitrap;AC=MS:1000484	1	1	20180507_OR16_Ag6_5607264_SA_MHC_HCD_clone1-IP1.raw	v1.1.0	NT=ms-proteomics;VV=v1.1.0	NT=human;VV=v1.1.0	NT=immunopeptidomics;VV=v1.0.0	manual curation	colorectal cancer

datasets/PXD016582/PXD016582-immunopeptidome.sdrf.tsv:2

• All four tumor clones are assigned biological replicate 1 on every run, while only the three injections per clone are distinguished as technical replicates. With the current disease-only factor, these are independent biological samples in the same colorectal cancer group; give T1/T3/T4/T5 distinct biological-replicate IDs (and keep N41 at 1), or make clone the factor group and document that design. As written, downstream analyses can collapse the tumor clones into one biological replicate.

Patient41_T1	Homo sapiens	colon	colorectal cancer	epithelial cell of large intestine	cell	adult	71Y	female	not available	Patient41	1	MHC class I protein complex	HLA-A*02:01;HLA-B*15:01;HLA-B*57:01;HLA-C*03:04;HLA-C*06:02	not available	W6/32	immunoaffinity purification	20180507_OR16_Ag6_5607264_SA_MHC_HCD_clone1-IP1	proteomic profiling by mass spectrometry	NT=Data-dependent acquisition;AC=PRIDE:0000627	NT=Q Exactive HF-X;AC=MS:1002877	NT=label free sample;AC=MS:1002038	NT=Cysteinyl;AC=UNIMOD:312;TA=C;MT=Variable	NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable	NT=unspecific cleavage;AC=MS:1001956	NT=beam-type collision-induced dissociation;AC=MS:1000422	35% NCE	not available	not available	2	3	100m/z	10% acetic acid	400m/z-650m/z	NT=orbitrap;AC=MS:1000484	1	1	20180507_OR16_Ag6_5607264_SA_MHC_HCD_clone1-IP1.raw	v1.1.0	NT=ms-proteomics;VV=v1.1.0	NT=human;VV=v1.1.0	NT=immunopeptidomics;VV=v1.0.0	manual curation	colorectal cancer

• Files reviewed: 1/1 changed files
• Comments generated: 2
• Review effort level: Lite (auto)

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