Suspension TRAPping Filter (sTRAP) Sample Preparation for Quantitative Proteomics in the Low µg Input Range Using a Plasmid DNA Micro-Spin Column: Analysis of the Hippocampus from the 5xFAD Alzheimer's Disease Mouse Model.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37174641", "kind": "science-record", "revision": 2, "content_hash": "sha256:d6d7a3f8104471b852c16c955594bbe2aa1a449c60cca6f11ce2a10455618fd7", "created_at": "2026-11-01T19:01:50Z", "updated_at": "2026-11-01T21:30:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Suspension TRAPping Filter (sTRAP) Sample Preparation for Quantitative Proteomics in the Low µg Input Range Using a Plasmid DNA Micro-Spin Column: Analysis of the Hippocampus from the 5xFAD Alzheimer's Disease Mouse Model.", "doi": "10.3390/cells12091242", "pmid": "37174641", "authors": ["Evangelia Thanou", "Frank Koopmans", "Débora Pita-Illobre", "Remco V Klaassen", "Berna Özer", "Ioannis Charalampopoulos", "August B Smit", "Ka Wan Li"], "journal": "Cells", "year": 2023, "abstract": "Suspension TRAPping filter (sTRAP) is an attractive sample preparation method for proteomics studies. The sTRAP protocol uses 5% SDS that maximizes protein solubilization. Proteins are trapped on a borosilicate glass membrane filter, where SDS is subsequently removed from the filter. After trypsin digestion, peptides are analyzed directly by LC-MS. Here, we demonstrated the use of a low-cost plasmid DNA micro-spin column for the sTRAP sample preparation of a dilution series of a synapse-enriched sample with a range of 10-0.3 µg. With 120 ng tryptic peptides loaded onto the Evosep LC system coupled to timsTOF Pro 2 mass spectrometer, we identified 5700 protein groups with 4% coefficient of variation (CoV). Comparing other sample preparation protocols, such as the in-gel digestion and the commercial Protifi S-TRAP with the plasmid DNA micro-spin column, the last is superior in both protein and peptide identification numbers and CoV. We applied sTRAP for the analysis of the hippocampal proteome from the 5xFAD mouse model of Alzheimer's disease and their wildtype littermates, and revealed 121 up- and 54 down-regulated proteins. Protein changes in the mutant mice point to the alteration of processes related to the immune system and Amyloid aggregation, which correlates well with the known major Alzheimer's-disease-related pathology. Data are available via ProteomeXchange with the identifier PXD041045.", "claims": [{"id": "claim-method", "statement": "Empirical Bayes moderated t-statistics with multiple testing correction by false discovery rate (FDR) ≤ 0.05, as implemented by the DEqMS function, was used as previously described [20].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37174641", "locator": "sections[8] \"2.6. Data Analysis\" paragraph 3", "quote": "Empirical Bayes moderated t-statistics with multiple testing correction by false discovery rate (FDR) ≤ 0.05, as implemented by the DEqMS function, was used as previously described [20]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics datasets generated during the current study are available in the PRIDE repository, with the identifier PXD041045.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37174641", "locator": "sections[20] \"Data Availability Statement\" paragraph 2", "quote": "The mass spectrometry proteomics datasets generated during the current study are available in the PRIDE repository, with the identifier PXD041045."}], "state": "complete"}, {"id": "claim-target-result", "statement": "With 120 ng tryptic peptides loaded onto the Evosep LC system coupled to timsTOF Pro 2 mass spectrometer, we identified 5700 protein groups with 4% coefficient of variation (CoV).", "kind": "quantitative", "target": {"value": 4.0, "unit": "per cent", "tolerance": null, "source": "With 120 ng tryptic peptides loaded onto the Evosep LC system coupled to timsTOF Pro 2 mass spectrometer, we identified 5700 protein groups with 4% coefficient of variation (CoV)."}, "evidence": [{"asset": "source:pmid:37174641", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "With 120 ng tryptic peptides loaded onto the Evosep LC system coupled to timsTOF Pro 2 mass spectrometer, we identified 5700 protein groups with 4% coefficient of variation (CoV)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "With 120 ng tryptic peptides loaded onto the Evosep LC system coupled to timsTOF Pro 2 mass spectrometer, we identified 5700 protein groups with 4% coefficient of variation (CoV).", "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:37174641"], "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. 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