relative_path	category	description	provenance	derived_from	compression	verification
raw/LFQ_Astral_DIA_15min_50ng_Human_01.raw	source_raw	ProteoBench Astral DIA technical replicate 1	ProteoBench DIA Ion Entrapment – Astral benchmark		none	preserve original filename
raw/LFQ_Astral_DIA_15min_50ng_Human_02.raw	source_raw	ProteoBench Astral DIA technical replicate 2	ProteoBench DIA Ion Entrapment – Astral benchmark		none	preserve original filename
raw/LFQ_Astral_DIA_15min_50ng_Human_03.raw	source_raw	ProteoBench Astral DIA technical replicate 3	ProteoBench DIA Ion Entrapment – Astral benchmark		none	preserve original filename
full_fasta/ProteoBenchFASTA_Entrapment_Human_with_contaminants_entrapment_pep.fasta	source_fasta	Full pre-digested target/entrapment peptide FASTA including contaminants	ProteoBench DIA Ion Entrapment – Astral benchmark		none	source input
full_fasta/ProteoBenchFASTA_Entrapment_Human_with_contaminants_entrapment.decoys.tsv.zst	derived_library	Predicted target/decoy OpenDIA assay library for the full FASTA	OpenDIA/OpenMS derived	full_fasta/ProteoBenchFASTA_Entrapment_Human_with_contaminants_entrapment_pep.fasta	zstd	adjacent .sha256
full_fasta/ProteoBenchFASTA_Entrapment_Human_with_contaminants_entrapment.decoys.tsv.zst.sha256	checksum	SHA-256 checksum for the full predicted target/decoy assay library	Generated during packaging	full_fasta/ProteoBenchFASTA_Entrapment_Human_with_contaminants_entrapment.decoys.tsv.zst	none	sha256sum -c
100K_sampled_fasta/ProteoBenchFASTA_Entrapment_Human_with_contaminants_entrapment_pep_100k_randomly_sampled.fasta	derived_fasta	Randomly sampled 100,000-entry subset of the pre-digested benchmark FASTA	Derived benchmark input	full_fasta/ProteoBenchFASTA_Entrapment_Human_with_contaminants_entrapment_pep.fasta	none	see opendia_results/meta/fasta.sha256
100K_sampled_fasta/ProteoBenchFASTA_Entrapment_Human_with_contaminants_entrapment_pep_100k_randomly_sampled.decoys.tsv.zst	derived_library	Predicted target/decoy OpenDIA assay library for the 100K sampled FASTA	OpenDIA/OpenMS derived	100K sampled FASTA	zstd	adjacent .sha256
100K_sampled_fasta/ProteoBenchFASTA_Entrapment_Human_with_contaminants_entrapment_pep_100k_randomly_sampled.decoys.tsv.zst.sha256	checksum	SHA-256 checksum for the 100K predicted target/decoy assay library	Generated during packaging	100K sampled assay library	none	sha256sum -c
100K_sampled_fasta/opendia_results/OpenDIA.results.tsv	analysis_result	Primary tabular OpenDIA result for the 100K sampled-FASTA analysis	OpenDIA/OpenMS derived	100K sampled FASTA + 3 ProteoBench RAW files	none	see meta/results_manifest.tsv
100K_sampled_fasta/opendia_results/LFQ_Astral_DIA_15min_50ng_Human_01_extracted.chrom.xic	analysis_intermediate	Extracted chromatogram artifact for RAW replicate 1	OpenDIA/OpenMS derived	raw/LFQ_Astral_DIA_15min_50ng_Human_01.raw	none	see run metadata
100K_sampled_fasta/opendia_results/LFQ_Astral_DIA_15min_50ng_Human_02_extracted.chrom.xic	analysis_intermediate	Extracted chromatogram artifact for RAW replicate 2	OpenDIA/OpenMS derived	raw/LFQ_Astral_DIA_15min_50ng_Human_02.raw	none	see run metadata
100K_sampled_fasta/opendia_results/LFQ_Astral_DIA_15min_50ng_Human_03_extracted.chrom.xic	analysis_intermediate	Extracted chromatogram artifact for RAW replicate 3	OpenDIA/OpenMS derived	raw/LFQ_Astral_DIA_15min_50ng_Human_03.raw	none	see run metadata
100K_sampled_fasta/opendia_results/logs/opendia.stdout.log	log	Captured OpenDIA standard output	OpenDIA run record	100K OpenDIA analysis	none	reproducibility record
100K_sampled_fasta/opendia_results/logs/opendia.stderr.log	log	Captured OpenDIA standard error	OpenDIA run record	100K OpenDIA analysis	none	reproducibility record
100K_sampled_fasta/opendia_results/logs/time.txt	log	Runtime/resource timing record	OpenDIA run record	100K OpenDIA analysis	none	reproducibility record
100K_sampled_fasta/opendia_results/meta/command.sh	metadata	Exact OpenDIA command used for the 100K analysis	OpenDIA run record	100K OpenDIA analysis	none	authoritative parameter record
100K_sampled_fasta/opendia_results/meta/exit_code.txt	metadata	OpenDIA process exit code	OpenDIA run record	100K OpenDIA analysis	none	successful run should record zero
100K_sampled_fasta/opendia_results/meta/fasta.sha256	checksum	SHA-256 identity of the 100K FASTA input	OpenDIA run record	100K sampled FASTA	none	SHA-256 checksum
100K_sampled_fasta/opendia_results/meta/opendia.helphelp.txt	metadata	Complete OpenDIA parameter/help surface from the build used	OpenDIA run record	OpenDIA executable/container	none	reproducibility record
100K_sampled_fasta/opendia_results/meta/raw_files.txt	metadata	List of RAW input files used in the OpenDIA run	OpenDIA run record	ProteoBench RAW files	none	reproducibility record
100K_sampled_fasta/opendia_results/meta/results_manifest.tsv	metadata	Manifest generated for OpenDIA result outputs	OpenDIA run record	100K OpenDIA analysis	none	reproducibility record
100K_sampled_fasta/opendia_results/meta/run_manifest.txt	metadata	OpenDIA run-level provenance and configuration summary	OpenDIA run record	100K OpenDIA analysis	none	authoritative run record
100K_sampled_fasta/opendia_results/meta/sif.sha256	checksum	SHA-256 identity of the Singularity image used for OpenDIA	OpenDIA run record	OpenDIA container	none	SHA-256 checksum