Add msproteomics test datasets#1953
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Public datasets for nf-core/msproteomics pipeline stub and integration testing: - 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 subset, E.coli+UPS1) - Module inputs: pre-computed intermediate files for unit testing individual modules - Samplesheets: CSV inputs for all workflow test profiles - Script: generate_test_subsets.sh for reproducible subset generation human_sp_subset.fasta contains 2000 proteins: 169 identified from DDA LFQ test spectra (HEK SILAC) + 1831 evenly-spaced entries for search space diversity. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Author
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@mashehu any other comments? |
Contributor
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going below 1000 proteins would not make sense? |
Author
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I did this. Now the fasta is 1.4Mb. |
Contributor
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ah, because it said 2000. would it still work if it is <100? |
Author
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any other comments? I can try but I am not sure from when fragpipe and diann will reject it. |
Author
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another question, what is the size limit of files? I thought it was 5 Mb and I did ensure all fasta files are under 5 Mb. |
Contributor
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we basically want it as small as possible. github has a limit of 7Mb, i think, but this repo has quite a lot of files in this range already |
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Summary
Public test datasets for the nf-core/msproteomics pipeline.
FASTA file sizes
ecoli_ups1_test.fastaerwinia_carotovora.fastaerwinia_uniprot.fastahuman_sp_subset.fastahuman_sp_subset.fastais 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