#1952 Add msproteomics test datasets Pull request opened by an-altosian Summary Public test datasets for the nf-core/msproteomics pipeline. • TMT: PRIDE PXD000001 (Erwinia carotovora, TMT6) — 2 mzML subsets • DDA LFQ: Zenodo 1051552 (Human SILAC) — 2 mzML subsets • DIA: CPTAC CCRCC (Human DIA) — 1 mzML subset • FASTA: UniProt reference databases (Erwinia, Human SwissProt 2000-protein subset, E.coli+UPS1) • Module inputs: Pre-computed intermediate files for unit testing individual modules • Samplesheets: CSV inputs for all workflow test profiles FASTA file sizes | File | Size | Proteins | | ------------------------ | ------ | -------- | | ecoli_ups1_test.fasta | 1.8 MB | — | | erwinia_carotovora.fasta | 1.6 MB | — | | erwinia_uniprot.fasta | 1.9 MB | — | | human_sp_subset.fasta | 1.4 MB | 2,000 |

human_sp_subset.fasta

is a smart subset: 169 proteins identified from the DDA LFQ test spectra (HEK SILAC) + 1,831 evenly-spaced SwissProt entries for search space diversity. Validated by running the full FragPipe DDA LFQ pipeline end-to-end (174 proteins identified at 1% FDR). Supersedes #1946 (closed due to force-push history issue). 🤖 Generated with Claude Code nf-core/test-datasets