Comparison of fractionation proteomics for local SWATH library building.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28664598", "kind": "science-record", "revision": 4, "content_hash": "sha256:d02ffa5df22ba248c98bceb9ad3bf86bf091f801daa4689d52f71f636b02d42b", "created_at": "2026-11-01T15:40:26Z", "updated_at": "2026-11-01T21:20:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comparison of fractionation proteomics for local SWATH library building.", "doi": "10.1002/pmic.201700052", "pmid": "28664598", "authors": ["Elisabeth Govaert", "Katleen Van Steendam", "Sander Willems", "Liesbeth Vossaert", "Maarten Dhaenens", "Dieter Deforce"], "journal": "Proteomics", "year": 2017, "abstract": "For data-independent acquisition by means of sequential window acquisition of all theoretical fragment ion spectra (SWATH), a reference library of data-dependent acquisition (DDA) runs is typically used to correlate the quantitative data from the fragment ion spectra with peptide identifications. The quality and coverage of such a reference library is therefore essential when processing SWATH data. In general, library sizes can be increased by reducing the impact of DDA precursor selection with replicate runs or fractionation. However, these strategies can affect the match between the library and SWATH measurement, and thus larger library sizes do not necessarily correspond to improved SWATH quantification. Here, three fractionation strategies to increase local library size were compared to standard library building using replicate DDA injection: protein SDS-PAGE fractionation, peptide high-pH RP-HPLC fractionation and MS-acquisition gas phase fractionation. The impact of these libraries on SWATH performance was evaluated in terms of the number of extracted peptides and proteins, the match quality of the peptides and the extraction reproducibility of the transitions. These analyses were conducted using the hydrophilic proteome of differentiating human embryonic stem cells. Our results show that SWATH quantitative results and interpretations are affected by choice of fractionation technique. Data are available via ProteomeXchange with identifier PXD006190.", "claims": [{"id": "claim-method", "statement": "Differential protein expression analysis between undiff and diff hESC was performed in MarkerView (Sciex) using a two‐sample t‐test of the normalized protein peak areas based on total area sums.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28664598", "locator": "sections[11] \"Data analysis\" paragraph 2", "quote": "Differential protein expression analysis between undiff and diff hESC was performed in MarkerView (Sciex) using a two‐sample t‐test of the normalized protein peak areas based on total area sums."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium 29 via the PRIDE 30 partner repository with the dataset identifier PXD006190.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28664598", "locator": "sections[22] \"Acknowledgment\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium 29 via the PRIDE 30 partner repository with the dataset identifier PXD006190."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Differential protein expression was evaluated by t-test, with significant results defined as p-value <0.05 and at least a 1.5-fold increase or decrease; the source data are available through ProteomeXchange under identifier PXD006190.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28664598", "locator": "sections[18] \"Differential protein expression analysis\" paragraph 2", "quote": "When a t‐test was performed for each protein between undiff and diff samples, this resulted in 363, 420, 358, and 387 proteins that were significantly different (p‐value <0.05) with at least 1.5‐fold increase or decrease for Lib_DDA, Lib_GP, Lib_RPRP and Lib_Gel, respectively."}, {"asset": "source:pmid:28664598", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD006190."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Differential protein expression was evaluated by t-test, with significant results defined as p-value <0.05 and at least a 1.5-fold increase or decrease; the source data are available through ProteomeXchange under identifier PXD006190.", "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:28664598"], "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:PXD006190"], "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:PXD006190"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28664598", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/pmic.201700052", "sha256": "sha256:d6f5d4937b7b3ad2ba415cdb539c9ede055a6d7ed452278833a2b5de14c5f344", "bytes": 44049, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/pmic.201700052", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5601298", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD006190", "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=PXD006190", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD006190", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium 29 via the PRIDE 30 partner repository with the dataset identifier PXD006190.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium 29 via the PRIDE 30 partner repository with the dataset identifier PXD006190.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Comparison of fractionation proteomics for local SWATH library building", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:28664598:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d5e82affd1ea0b6166798a6d45764d411ad89b3ea73254b5fe75dbb9a91dbb6a", "bytes": 983, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#pmic12663-tbl-0001", "version": null, "note": "Overview of the benefits and drawbacks of each fractionation method for local reference library building evaluated in this study", "structure": {"pmcid": "PMC5601298", "section_index": 18, "section_title": "Differential protein expression analysis", "row_count": 11, "column_count": 5}, "table": {"label": "Table 1", "caption": "Overview of the benefits and drawbacks of each fractionation method for local reference library building evaluated in this study", "rows": [["", "DDA replicate injection", "MS‐acquisition GP fractionation", "Peptide RPRP fractionation", "Protein SDS‐PAGE fractionation"], ["Cost‐effectiveness", "++", "++", "‐", "+"], ["Time investment", "++", "++", "‐", "‐"], ["Number of proteins in library", "‐", "+", "+", "++"], ["Number of peptides in library (targeted)", "‐", "++", "+", "++"], ["Number of extracted proteins", "‐", "+", "+", "++"], ["Number of extracted peptides FDR < 1%", "‐", "++", "+", "++"], ["Number of extracted proteins CV < 20%", "+", "+", "+", "+"], ["Number of extracted peptides CV < 20%", "+", "+", "+", "+"], ["Number of extracted transitions CV < 20%", "+", "+", "+", "+"], ["Extraction of core pluripotency markers", "+", "++", "‐", "++"]], "row_count": 11, "column_count": 5, "numeric_cells": 4, "header_rows": 1, "locator": "section[18]/table-wrap[1]#pmic12663-tbl-0001"}}], "gaps": ["asset:data:geo:PXD006190 not downloaded", "asset:data:geo:PXD006190 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "two-sample t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differential protein expression analysis between undiff and diff hESC was performed in MarkerView (Sciex) using a two‐sample t‐test of the normalized protein peak areas based on total area sums."}}], "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 (two-sample t-test), 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": ["PXD006190"], "resolved_accessions": ["PXD006190"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium 29 via the PRIDE 30 partner repository with the dataset identifier PXD006190."], "basis": "The paper names PXD006190 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:28664598", "data:geo:PXD006190", "asset:table:pmid:28664598:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD006190"]}, "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": "2026-10-31T18:31:25Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 89554, "completion_tokens": 2927, "cached_tokens": 2088}}, "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:28664598", "type": "paper", "label": "pmid:28664598"}, {"id": "source:pmid:28664598", "type": "manuscript", "label": "PMID 28664598 full text"}, {"id": "data:geo:PXD006190", "type": "dataset", "label": "GEO PXD006190"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28664598", "type": "paper", "label": "pmid:28664598"}, {"id": "source:pmid:28664598", "type": "manuscript", "label": "PMID 28664598 full text"}, {"id": "data:geo:PXD006190", "type": "dataset", "label": "GEO PXD006190"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28664598", "type": "extraction", "used": ["source:pmid:28664598"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD006190", "type": "accession_resolution", "used": ["data:geo:PXD006190"], "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:28664598", "parent_hash": "sha256:8d0c257b700a0ca6b05dd95c27872e1f5df8fe0f46845e5712442647f4fdbf09", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:PXD006190 licence not read", "asset:data:geo:PXD006190 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"]}