Use of Hybrid Data-Dependent and -Independent Acquisition Spectral Libraries Empowers Dual-Proteome Profiling.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33467856", "kind": "science-record", "revision": 6, "content_hash": "sha256:9821fee9c8b9024ba4b1ad3680355abeca53cc229e5866bd3c16274d1895c3e5", "created_at": "2026-11-01T15:41:23Z", "updated_at": "2026-11-01T21:24:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Use of Hybrid Data-Dependent and -Independent Acquisition Spectral Libraries Empowers Dual-Proteome Profiling.", "doi": "10.1021/acs.jproteome.0c00350", "pmid": "33467856", "authors": ["Patrick Willems", "Ursula Fels", "An Staes", "Kris Gevaert", "Petra Van Damme"], "journal": "Journal of proteome research", "year": 2021, "abstract": "In the context of bacterial infections, it is imperative that physiological responses can be studied in an integrated manner, meaning a simultaneous analysis of both the host and the pathogen responses. To improve the sensitivity of detection, data-independent acquisition (DIA)-based proteomics was found to outperform data-dependent acquisition (DDA) workflows in identifying and quantifying low-abundant proteins. Here, by making use of representative bacterial pathogen/host proteome samples, we report an optimized hybrid library generation workflow for DIA mass spectrometry relying on the use of data-dependent and in silico-predicted spectral libraries. When compared to searching DDA experiment-specific libraries only, the use of hybrid libraries significantly improved peptide detection to an extent suggesting that infection-relevant host-pathogen conditions could be profiled in sufficient depth without the need of a priori bacterial pathogen enrichment when studying the bacterial proteome. Proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD017904 and PXD017945.", "claims": [{"id": "claim-method", "statement": "Subsequently, we used the obtained Percolator score as the discriminant score for MAYU FDR estimation for peptides matching non-ambiguously to human Swiss-Prot or Salmonella proteins.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33467856", "locator": "sections[13] \"Hybrid Library Construction\" paragraph 2", "quote": "Subsequently, we used the obtained Percolator score as the discriminant score for MAYU FDR estimation for peptides matching non-ambiguously to human Swiss-Prot or Salmonella proteins."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE58 partner repository with the dataset identifier PXD017904 for DDA artificial mixtures and Salmonella pre-fractionated samples and with the dataset identifier PXD017945 for the DIA artificial mixtures. In addition, the generated spectral libraries, FASTA databases, and search results are organized in the Open Science Framework (OSF) project page59 and are available at https://osf.io/u96bk/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33467856", "locator": "sections[28] \"Notes\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE58 partner repository with the dataset identifier PXD017904 for DDA artificial mixtures and Salmonella pre-fractionated samples and with the dataset identifier PXD017945 for the DIA artificial mixtures. In addition, the generated spectral libraries, FASTA databases, and search results are organized in the Open Science Framework (OSF) project page59 and are available at https://osf.io/u96bk/."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:33467856"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD017904"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD017904"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33467856", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1021/acs.jproteome.0c00350", "sha256": "sha256:7986d5da341c097afb867f819833536812e6c55a5d0af649f31fd9173bfec0b0", "bytes": 76996, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1021/acs.jproteome.0c00350", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7871992", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD017904", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD017904", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD017904", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE58 partner repository with the dataset identifier PXD017904 for DDA artificial mixtures and Salmonella pre-fractionated samples and with the dataset identifier PXD017945 for the DIA artificial mixtures. In addition, the generated spectral libraries, FASTA databases, and search results are organized in the Open Science Framework (OSF) project page59 and are available at https://osf.io/u96bk/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE58 partner repository with the dataset identifier PXD017904 for DDA artificial mixtures and Salmonella pre-fractionated samples and with the dataset identifier PXD017945 for the DIA artificial mixtures. In addition, the generated spectral libraries, FASTA databases, and search results are organized in the Open Science Framework (OSF) project page59 and are available at https://osf.io/u96bk/.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Data-dependent and independent acquisition of complex human-Salmonella mixed proteomes", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PXD017945", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD017945", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD017945", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE58 partner repository with the dataset identifier PXD017904 for DDA artificial mixtures and Salmonella pre-fractionated samples and with the dataset identifier PXD017945 for the DIA artificial mixtures. In addition, the generated spectral libraries, FASTA databases, and search results are organized in the Open Science Framework (OSF) project page59 and are available at https://osf.io/u96bk/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE58 partner repository with the dataset identifier PXD017904 for DDA artificial mixtures and Salmonella pre-fractionated samples and with the dataset identifier PXD017945 for the DIA artificial mixtures. In addition, the generated spectral libraries, FASTA databases, and search results are organized in the Open Science Framework (OSF) project page59 and are available at https://osf.io/u96bk/.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Data-dependent and independent acquisition of complex human-Salmonella mixed proteomes", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD017904 not downloaded", "asset:data:geo:PXD017904 licence not read", "asset:data:geo:PXD017945 not downloaded", "asset:data:geo:PXD017945 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "MAYU false discovery rate estimation using the Percolator score", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Subsequently, we used the obtained Percolator score as the discriminant score for MAYU FDR estimation for peptides matching non-ambiguously to human Swiss-Prot or Salmonella proteins."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (MAYU false discovery rate estimation using the Percolator score), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD017904", "PXD017945"], "resolved_accessions": ["PXD017904", "PXD017945"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE58 partner repository with the dataset identifier PXD017904 for DDA artificial mixtures and Salmonella pre-fractionated samples and with the dataset identifier PXD017945 for the DIA artificial mixtures. In addition, the generated spectral libraries, FASTA databases, and search results are organized in the Open Science Framework (OSF) project page59 and are available at https://osf.io/u96bk/."], "basis": "The paper names PXD017904, PXD017945 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:33467856", "data:geo:PXD017904"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD017904"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:26:26Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 57916, "completion_tokens": 2164, "cached_tokens": 776}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:33467856", "type": "paper", "label": "pmid:33467856"}, {"id": "source:pmid:33467856", "type": "manuscript", "label": "PMID 33467856 full text"}, {"id": "data:geo:PXD017904", "type": "dataset", "label": "GEO PXD017904"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33467856", "type": "paper", "label": "pmid:33467856"}, {"id": "source:pmid:33467856", "type": "manuscript", "label": "PMID 33467856 full text"}, {"id": "data:geo:PXD017904", "type": "dataset", "label": "GEO PXD017904"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33467856", "type": "extraction", "used": ["source:pmid:33467856"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD017904", "type": "accession_resolution", "used": ["data:geo:PXD017904"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:33467856", "parent_hash": "sha256:a1fae2b206dcd56833641ff0272fc829491117f3cdc1f11f9e8754aae50bbf11", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD017904 licence not read", "asset:data:geo:PXD017904 not downloaded", "asset:data:geo:PXD017945 licence not read", "asset:data:geo:PXD017945 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["d hybrid library generation workflow for DIA mass spectrometry relying on the use of data-dependent and in", "on, data-independent acquisition (DIA)-based proteomics was found to outperform data-dependent acqui", "chment when studying the bacterial proteome. Proteomics data have been deposited to the ProteomeXcha"], "order_basis": "paper_text_order:351", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["lection, Manassas, VA, USA; ATCC CCL-2) were cultured in GlutaMAX containing Dulbecco’s modified Eagl", "C in a humidified atmosphere with 5% CO2 and passaged at a 1:8 ratio every 4 days. Proteome Extrac", "Experimental Procedures HeLa Cell Culture HeLa cells (epithelial cervix a", "Experimental Procedures HeLa Cell Culture HeLa cells (epithelial cervix adenocarcinoma, Ame"], "order_basis": "paper_text_order:1274", "id": "assay:2"}]}