New label-free methods for protein relative quantification applied to the investigation of an animal model of Huntington Disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32886703", "kind": "science-record", "revision": 7, "content_hash": "sha256:c9436a070d9a430fdb179472f5788185ad5b02a3cca83d3d2e7ccc0f0b1d4046", "created_at": "2026-11-01T15:41:09Z", "updated_at": "2026-11-01T22:02:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "New label-free methods for protein relative quantification applied to the investigation of an animal model of Huntington Disease.", "doi": "10.1371/journal.pone.0238037", "pmid": "32886703", "authors": ["Flora Cozzolino", "Alfredo Landolfi", "Ilaria Iacobucci", "Vittoria Monaco", "Marianna Caterino", "Simona Celentano", "Chiara Zuccato", "Elena Cattaneo", "Maria Monti"], "journal": "PloS one", "year": 2020, "abstract": "Spectral Counts approaches (SpCs) are largely employed for the comparison of protein expression profiles in label-free (LF) differential proteomics applications. Similarly, to other comparative methods, also SpCs based approaches require a normalization procedure before Fold Changes (FC) calculation. Here, we propose new Complexity Based Normalization (CBN) methods that introduced a variable adjustment factor (f), related to the complexity of the sample, both in terms of total number of identified proteins (CBN(P)) and as total number of spectral counts (CBN(S)). Both these new methods were compared with the Normalized Spectral Abundance Factor (NSAF) and the Spectral Counts log Ratio (Rsc), by using standard protein mixtures. Finally, to test the robustness and the effectiveness of the CBNs methods, they were employed for the comparative analysis of cortical protein extract from zQ175 mouse brains, model of Huntington Disease (HD), and control animals (raw data available via ProteomeXchange with identifier PXD017471). LF data were also validated by western blot and MRM based experiments. On standard mixtures, both CBN methods showed an excellent behavior in terms of reproducibility and coefficients of variation (CVs) in comparison to the other SpCs approaches. Overall, the CBN(P) method was demonstrated to be the most reliable and sensitive in detecting small differences in protein amounts when applied to biological samples.", "claims": [{"id": "claim-method", "statement": "Mass spectrometry data (LF) statistical significance was determined by the unpaired Student’s t-test and differences were considered statistically significant at Benjamini-Hochberg corrected p-value (FDR)<0.05 [44].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32886703", "locator": "sections[11] \"Statistical analyses\" paragraph 2", "quote": "Mass spectrometry data (LF) statistical significance was determined by the unpaired Student’s t-test and differences were considered statistically significant at Benjamini-Hochberg corrected p-value (FDR)<0.05 [44]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with identifier PXD017471.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32886703", "locator": "sections[21] \"Data Availability\" paragraph 2", "quote": "Data are available via ProteomeXchange with identifier PXD017471."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:32886703"], "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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analysis.", "rows": [["Pathways Description", "Observed Gene Count (NSAF)", "FDR", "Observed Gene Count (RSC)", "FDR", "Observed Gene Count (CBN(P))", "FDR", "Observed Gene Count (CBN(S))", "FDR"], ["Metabolic pathways", "19", "2.62E-09", "42", "1.10E-09", "22", "2.30E-06", "42", "1.51E-10"], ["Oxidative phosphorylation", "7", "0.0037", "14", "9.68E-09", "7", "0.000105", "12", "7.09E-07"], ["Parkinson's disease", "9", "0.00049", "14", "1.77E-08", "8", "1.53E-05", "12", "1.11E-06"], ["Huntington's disease", "9", "0.00156", "14", "2.78E-07", "9", "9.82E-06", "13", "1.24E-06"], ["Alzheimer's disease", "9", "0.00111", "13", "8.40E-07", "7", "0.000397", "12", "3.94E-06"], ["Calcium signaling pathway", "8", "0.00412", "7", "0.0328", "7", "0.000566", "8", "0.0109"], ["Val, Leu and Ile degradation", "6", "0.00049", "5", "0.00648", "3", "0.0269", "5", "0.00578"], ["cGMP-PKG signaling pathway", "8", "0.0037", "8", "0.0094", "5", "0.02", "7", "0.0247"], ["Fatty acid degradation", "5", "0.00194", 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Similarly, to other comparativ", "tion of Spectral Counts data in differential proteomics experiments to calculate the relative Fold C", "isting normalization methods in differential proteomics experiments using the label-free procedure a", "plication of CBN methods to the differential proteomics analysis of samples from cerebral cortex fro"], "order_basis": "paper_text_order:222", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["lysis of cortical protein extract from zQ175 mouse brains, model of Huntington Disease (HD), an", "d proteins with all methods in the WT and HD mouse model.(A) The histogram shows for each method the", "whose expression was instead decreased in HD mice were evaluated on total protein extracts of three", "oteins differentially expressed in WT and HD mouse model.(A) Western blot assays performed on total p"], "order_basis": "paper_text_order:984", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["r PXD017471). LF data were also validated by western blot and MRM based experiments. On standard mixtu", "teins by two independent methodologies, i.e. western blot analyses and Multiple Reaction Monitoring (M", "itoring (MRM) mass spectrometry analysis. In western blot assays (Fig 5A), the expression levels of IR", "ially expressed in WT and HD mouse model.(A) Western blot assays performed on total protein extracts f"], "order_basis": "paper_text_order:1151", "id": "assay:3"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Mass spectrometry data (LF) statistical significance was determined by the unpaired Student’s t-test and differences were considered statistically significant at Benjamini-Hochberg corrected p-value (FDR)<0.05 [44]."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}