SWATH-MS data of Drosophila melanogaster proteome dynamics during embryogenesis.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27844044", "kind": "science-record", "revision": 3, "content_hash": "sha256:8904c54787b20c8991d39c7fa6333fb003536d3de3cbb0b22fe656cb85aadcc5", "created_at": "2026-11-01T15:40:21Z", "updated_at": "2026-11-01T21:20:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "SWATH-MS data of Drosophila melanogaster proteome dynamics during embryogenesis.", "doi": "10.1016/j.dib.2016.10.009", "pmid": "27844044", "authors": ["Bertrand Fabre", "Dagmara Korona", "Daniel J H Nightingale", "Steven Russell", "Kathryn S Lilley"], "journal": "Data in brief", "year": 2016, "abstract": "Embryogenesis is one of the most important processes in the life of an animal. During this dynamic process, progressive cell division and cellular differentiation are accompanied by significant changes in protein expression at the level of the proteome. However, very few studies to date have described the dynamics of the proteome during the early development of an embryo in any organism. In this dataset, we monitor changes in protein expression across a timecourse of more than 20 h of Drosophila melanogaster embryonic development. Mass-spectrometry data were produced using a SWATH acquisition mode on a Sciex Triple-TOF 6600. A spectral library built in-house was used to analyse these data and more than 1950 proteins were quantified at each embryonic timepoint. The files presented here are a permanent digital map and can be reanalysed to test against new hypotheses. The data have been deposited with the ProteomeXchange Consortium with the dataset identifier PRIDE: PXD0031078.", "claims": [{"id": "claim-method", "statement": "C) Volcano-plot representing the Benjamini–Hochberg corrected p-value as a function of the Log2 Fold Change for each protein between each timepoint and the 0–4.5 h timepoint.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27844044", "locator": "sections[5] \"Data\" paragraph 3", "quote": "C) Volcano-plot representing the Benjamini–Hochberg corrected p-value as a function of the Log2 Fold Change for each protein between each timepoint and the 0–4.5 h timepoint."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All the mass spectrometry data have been deposited with the ProteomeXchange [6] Consortium via the PRIDE partner repository with the dataset identifier PRIDE: PXD003178.\nThe results from the SWATH analysis of the time course experiment are provided as a Supplementary Table.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27844044", "locator": "sections[12] \"Data availability\" paragraphs 1-3", "quote": "All the mass spectrometry data have been deposited with the ProteomeXchange [6] Consortium via the PRIDE partner repository with the dataset identifier PRIDE: PXD003178.\nThe results from the SWATH analysis of the time course experiment are provided as a Supplementary Table."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using SWATH-MS and Benjamini–Hochberg-corrected p-values, the study quantified more than 1,950 proteins at each embryonic timepoint across more than 20 hours of Drosophila development, with the source data deposited in PRIDE under PXD0031078.", "kind": "quantitative", "target": {"value": 2.0, "unit": "fold change", "tolerance": null, "source": "Volcano-plot representing the Benjamini–Hochberg corrected p-value as a function of the Log2 Fold Change for each protein between each timepoint and the 0–4.5 h timepoint."}, "evidence": [{"asset": "source:pmid:27844044", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data have been deposited with the ProteomeXchange Consortium with the dataset identifier PRIDE: PXD0031078."}, {"asset": "source:pmid:27844044", "locator": "sections[5] \"Data\" paragraph 3", "quote": "Volcano-plot representing the Benjamini–Hochberg corrected p-value as a function of the Log2 Fold Change for each protein between each timepoint and the 0–4.5 h timepoint."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Using SWATH-MS and Benjamini–Hochberg-corrected p-values, the study quantified more than 1,950 proteins at each embryonic timepoint across more than 20 hours of Drosophila development, with the source data deposited in PRIDE under PXD0031078.", "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:27844044"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:27844044", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2016.10.009", "sha256": "sha256:e8fda798c51328724f5880ad9b9538a02ef5859f3e318ccf883f096db3d1de73", "bytes": 14815, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2016.10.009", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5097952", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Benjamini–Hochberg correction", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "C) Volcano-plot representing the Benjamini–Hochberg corrected p-value as a function of the Log2 Fold Change for each protein between each timepoint and the 0–4.5 h timepoint."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": null, "expected_value": 2.0, "unit": "fold change", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "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": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Benjamini–Hochberg correction), 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": "R4", "reachable": false, "accessions": ["PRIDE: PXD003178", "PRIDE: PXD0031078"], "resolved_accessions": [], "statements": ["All the mass spectrometry data have been deposited with the ProteomeXchange [6] Consortium via the PRIDE partner repository with the dataset identifier PRIDE: PXD003178.\nThe results from the SWATH analysis of the time course experiment are provided as a Supplementary Table."], "basis": "The paper names PRIDE: PXD003178, PRIDE: PXD0031078, but the accession does not resolve in the repository (no reason recorded, no reason recorded), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:27844044"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:29:58Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 37412, "completion_tokens": 4318, "cached_tokens": 1824}}, "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:27844044", "type": "paper", "label": "pmid:27844044"}, {"id": "source:pmid:27844044", "type": "manuscript", "label": "PMID 27844044 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:27844044", "type": "paper", "label": "pmid:27844044"}, {"id": "source:pmid:27844044", "type": "manuscript", "label": "PMID 27844044 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-27844044", "type": "extraction", "used": ["source:pmid:27844044"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:27844044", "parent_hash": "sha256:53542b327b3db2e211b50a8ca31ec499c3aeff442e930f768bf1ceed8e393336", "fork_of": null, "generation": 2}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"]}