Add SDRF annotation for PXD058436 (MHCquant2 immunopeptidomics)

[jonasscheid]

Dataset

PXD058436 — MHCquant2 refines immunopeptidomics tumor antigen discovery (Scheid J et al., Genome Biol 2025;26(1):290). Homo sapiens benign-tissue HLA class I & II immunopeptidome atlas, timsTOF Pro 2, DDA/PASEF.

• PX landing: https://www.ebi.ac.uk/pride/archive/projects/PXD058436
• Publication: https://doi.org/10.1186/s13059-025-03763-8 (PMID 40983925, PMC12455830)

What this adds

datasets/PXD058436/PXD058436.sdrf.tsv — 633 runs (312 HLA class I + 321 class II), 39 columns.
Templates: ms-proteomics 1.1.0 + human 1.1.0 + immunopeptidomics 1.0.0 (declared via comment[sdrf template]).

Annotation basis

• Row set keyed to the 633 deposited mzML filenames (donor_tissue_class_techRep); tissue mapped to UBERON, verified via OLS.
• Per-donor HLA genotypes converted to IPD-IMGT/HLA notation.
• Antibody enrichment (W6/32 class I; Tu-39/L243 class II), immunoaffinity purification, and instrument/acquisition detail taken from the paper Methods and PRIDE protocols.
• Agent-assisted annotation using sdrf-skills.

Flagged for reviewers

• DN05 donor code carries two distinct genotypes in the submitter draft; resolved to the per-donor consensus and noted.
• One submitter-draft filename was malformed (DN11_Cerebellum_techRep4.mzML, missing class token); aligned to the deposited DN11_Cerebellum_classII_techRep4.mzML.
• Demographics (age/sex/ancestry) not reported in the publication; set to not available.

Validation

parse_sdrf validate-sdrf (git main + ontology) with the three templates passes cache-only and live OLS: Everything seems to be fine.

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