#1946 Add msproteomics test datasets Pull request opened by an-altosian Summary • Test datasets for the nf-core/msproteomics pipeline stub and integration tests • 24 files across 5 categories: spectra, databases, module inputs, samplesheets, and tooling • All data derived from publicly available sources (PRIDE, Zenodo, CPTAC, UniProt) with no proprietary data • Includes a regeneration script (

generate_test_subsets.sh

) for reproducibility Data Sources Spectra (5 files) | File | Source | Accession | Description | | --------------------------------- | ------ | --------- | ---------------------------------------------- | | spectra/tmt_erwinia_subset.mzML | PRIDE | PXD000001 | Erwinia carotovora, TMT6-labeled | | spectra/tmt_erwinia_subset_2.mzML | PRIDE | PXD000001 | Erwinia carotovora, TMT6-labeled (replicate 2) | | spectra/dda_silac_subset.mzML | Zenodo | 1051552 | Human SILAC, DDA label-free | | spectra/dda_silac_subset_2.mzML | Zenodo | 1051552 | Human SILAC, DDA label-free (replicate 2) | | spectra/dia_cptac_subset.mzML | CPTAC | CCRCC | Human DIA | Databases (4 files) | File | Source | Description | | ---------------------------------- | ------- | ---------------------------------------------- | | databases/erwinia_carotovora.fasta | UniProt | Erwinia carotovora proteome | | databases/erwinia_uniprot.fasta | UniProt | Erwinia carotovora (UniProt-formatted headers) | | databases/human_sp_subset.fasta | UniProt | Human Swiss-Prot subset | | databases/ecoli_ups1_test.fasta | UniProt | E. coli + UPS1 spike-in | Module Inputs (9 files) Pre-computed intermediates generated by running FragPipe 24.0 toolchain on the public test data, enabling module-level testing without running upstream steps: | File | Module(s) Supported | | ----------------------------------------------------------- | ------------------------------------ | | module_inputs/tmt_erwinia_subset_msfragger.pepXML | MSBooster, PeptideProphet | | module_inputs/tmt_erwinia_subset.pin | Percolator | | module_inputs/interact-tmt_erwinia_subset.pep.xml | ProteinProphet | | module_inputs/tmt_erwinia_subset_percolator_target_psms.tsv | Philosopher Filter | | module_inputs/tmt_erwinia_subset_percolator_decoy_psms.tsv | Philosopher Filter | | module_inputs/psm.tsv | IonQuant, TMTIntegrator, PTMShepherd | | module_inputs/peptide.tsv | IonQuant, TMTIntegrator | | module_inputs/crystalc_test.pepXML | Crystal-C | | module_inputs/crystalc_test.mzML | Crystal-C | Samplesheets (4 files) | File | Workflow | | ----------------------------- | ----------------------------- | | samplesheets/test_dia.csv | DIA (DIA-NN) | | samplesheets/test_dda_lfq.csv | DDA label-free quantification | | samplesheets/test_tmt.csv | TMT label check | | samplesheets/test_tmtq.csv | TMT quantification | Tooling (2 files) | File | Purpose | | ------------------------ | ------------------------------------------------------------ | | generate_test_subsets.sh | Script to regenerate subsetted test data from public sources | | README.md | Documentation for the test datasets branch | Pipeline Modules Supported • File conversion: ThermoRawFileParser (spectra mzML files) • Database search: MSFragger (spectra + FASTA databases) • Rescoring: MSBooster (pepXML inputs) • Validation: Percolator (PIN inputs), PeptideProphet (pepXML inputs) • Protein inference: ProteinProphet (interact pepXML inputs) • Filtering: Philosopher Filter (Percolator TSV inputs) • Quantification: IonQuant, TMTIntegrator (PSM/peptide TSVs) • PTM analysis: PTMShepherd (PSM TSV), Crystal-C (pepXML + mzML) • DIA analysis: DIA-NN (DIA spectra + FASTA) • Spectral library: EasyPQP/SpecLibGen (search outputs) 🤖 Generated with Claude Code nf-core/test-datasets