Quantitative Label-Free Comparison of the Metabolic Protein Fraction in Old and Modern Italian Wheat Genotypes by a Shotgun Approach.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33946829", "kind": "science-record", "revision": 8, "content_hash": "sha256:e84bb6151a413c9bcc3c40b0347ef58cd2103397ebe1b2e765ae38a1dea79ed5", "created_at": "2026-11-01T15:41:34Z", "updated_at": "2026-11-01T22:46:38Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Quantitative Label-Free Comparison of the Metabolic Protein Fraction in Old and Modern Italian Wheat Genotypes by a Shotgun Approach.", "doi": "10.3390/molecules26092596", "pmid": "33946829", "authors": ["Antonella Di Francesco", "Vincenzo Cunsolo", "Rosaria Saletti", "Birte Svensson", "Vera Muccilli", "Pasquale De Vita", "Salvatore Foti"], "journal": "Molecules (Basel, Switzerland)", "year": 2021, "abstract": "Wheat represents one of the most important cereals for mankind. However, since wheat proteins are also the causative agent of several adverse reactions, during the last decades, consumers have shown an increasing interest in the old wheat genotypes, which are generally perceived as more \"natural\" and healthier than the modern ones. Comparison of nutritional value for modern and old wheat genotypes is still controversial, and to evaluate the real impact of these foods on human health comparative experiments involving old and modern genotypes are desirable. The nutritional quality of grain is correlated with its proteomic composition that depends on the interplay between the genetic characteristics of the plant and external factors related to the environment. We report here the label-free shotgun quantitative comparison of the metabolic protein fractions of two old Sicilian landraces (Russello and Timilia) and the modern variety Simeto, from the 2010-2011 and 2011-2012 growing seasons. The overall results show that Timilia presents the major differences with respect to the other two genotypes investigated. These differences may be related to different defense mechanisms and some other peculiar properties of these genotypes. On the other hand, our results confirm previous results leading to the conclusion that with respect to a nutritional value evaluation, there is a substantial equivalence between old and modern wheat genotypes. Data are available via ProteomeXchange with identifier <PXD024204>.", "claims": [{"id": "claim-method", "statement": "A protein was quantified when: (i) at least two of its unique peptides satisfied the parameters above reported; (ii) was identified in a minimum of five out of nine nanoLC-MS/MS runs per flour sample; and (iii) had a p-value < 0.05 and a significance ≥ 20 (significance method ANOVA; the significance score was calculated as the −10log10 of the significance testing p-value).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33946829", "locator": "sections[10] \"4.5. Label-Free Quantification\" paragraph 2", "quote": "A protein was quantified when: (i) at least two of its unique peptides satisfied the parameters above reported; (ii) was identified in a minimum of five out of nine nanoLC-MS/MS runs per flour sample; and (iii) had a p-value < 0.05 and a significance ≥ 20 (significance method ANOVA; the significance score was calculated as the −10log10 of the significance testing p-value)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Not applicable.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33946829", "locator": "sections[17] \"Institutional Review Board Statement\" paragraph 2", "quote": "Not applicable."}], "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:33946829"], "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:PXD024204"], "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:PXD024204"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33946829", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/molecules26092596", "sha256": "sha256:4442d0ded8262e2472f4d397b4a1bbba203425089bb6219b7515b648170e58fe", "bytes": 55717, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/molecules26092596", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8124627", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD024204", "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=PXD024204", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD024204", "version": null, "note": "Not applicable.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Not applicable.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Quantitative Label-free Comparison of the Metabolic Protein Fraction in Old and Modern Wheat Italian Genotypes by a Shotgun Approach", "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:33946829:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c258f05683d37bd88c5a61c1c02a92a8b8f7460871e2271aea72ac84a105a7b1", "bytes": 1698, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#molecules-26-02596-t001", "version": null, "note": "Protein profile heat map (cell color represents the fold change observed across the genotype investigated). Each cell also reports the corresponding fold change observed in the two growing seasons. Proteins marked with an asterisk were also detected as intra-genotype DAPs. For details see Table 2.", "structure": {"pmcid": "PMC8124627", "section_index": 3, "section_title": "Differentially Abundant Proteins Genotype-Related", "row_count": 25, "column_count": 6}, "table": {"label": "Table 1", "caption": "Protein profile heat map (cell color represents the fold change observed across the genotype investigated). Each cell also reports the corresponding fold change observed in the two growing seasons. Proteins marked with an asterisk were also detected as intra-genotype DAPs. For details see Table 2.", "rows": [["Proteins", "Gene Code", "Growing Season 2010/2011", "Growing Season 2011/2012", "Fold Change"], ["Fold Change", "Fold Change"], ["Russello vs. Simeto", "", "", "", "", "64"], ["Avenin-like b1", "AVLB1", "0.12", "0.12"], ["Oil body-associated protein 1A", "OBP1A", "4.75", "9.73"], ["Serpin-Z1C", "SPZ1C *", "0.4", "0.21"], ["Timilia vs. Simeto", "", "", ""], ["26 kDa endochitinase 2", "CHI2", "0.44", "0.41"], ["a-amylase inhibitor 0.28", "IAA2", "64", "64"], ["Antifungal protein R (Fragment)", "THHR", "0.27", "0.32"], ["Avenin-like b1", "AVLB1 *", "3.33", "2.5"], ["L-ascorbate peroxidase 2 cytosolic", "APX2 *", "5.15", "2.32"], ["Oil body-associated protein 1A", "OBP1A", "4.6", "9.09"], ["Subtilisin-chymotrypsin inhibitor WSCI", "ICIW", "6.61", "4.67", "1"], ["Sucrose synthase 1", "SUS1", "6.31", "3.95"], ["Sucrose synthase 3", "SUS3", "3.13", "2.1"], ["Timilia vs. Russello", "", "", ""], ["26 kD aendochitinase 2", "CHI2", "0.27", "0.33"], ["a-amylase inhibitor WDAI-3 (Fragment)", "IAA3 *", "0.39", "0.39"], ["Avenin-like b1", "AVLB1 *", "38.49", "25.39"], ["Linoleate 9S-lipoxygenase 1", "LOX1", "2.42", "2.28"], ["Serpin-Z2A", "SPZ2A", "0.02", "0.02"], ["Subtilisin-chymotrypsin inhibitor WSCI", "ICIW", "6.74", "5.81"], ["Sucrose synthase 1", "SUS1", "3.36", "2.05"], ["Sucrose synthase 3", "SUS3", "3.11", "2.3"]], "row_count": 25, "column_count": 6, "numeric_cells": 56, "header_rows": 2, "locator": "section[3]/table-wrap[1]#molecules-26-02596-t001"}}, {"id": "asset:table:pmid:33946829:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2965afa3c49282c0bb6d99fc55218bcb9b8e31516f5f0975a889aaaf9db3d7f2", "bytes": 4479, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[2]#molecules-26-02596-t002", "version": null, "note": "List of the proteins detected as DAPs in both the growing seasons investigated: Russello vs. Simeto; Timilia vs. Simeto; Timilia vs. Russello. For each protein is reported: Accession Number as used in the Uniprot database; gene code; organism; protein description; the fold change (if ≤0.5 or ≥2); p-value observed in the growing seasons 2010–2011 and 2011–2012; significance; the number of the characterized peptides; the number of unique peptides, and the biological process in which it is involved. Proteins that were also detected as intra-genotype DAPs are reported in italics.", "structure": {"pmcid": "PMC8124627", "section_index": 3, "section_title": "Differentially Abundant Proteins Genotype-Related", "row_count": 25, "column_count": 16}, "table": {"label": "Table 2", "caption": "List of the proteins detected as DAPs in both the growing seasons investigated: Russello vs. Simeto; Timilia vs. Simeto; Timilia vs. Russello. For each protein is reported: Accession Number as used in the Uniprot database; gene code; organism; protein description; the fold change (if ≤0.5 or ≥2); p-value observed in the growing seasons 2010–2011 and 2011–2012; significance; the number of the characterized peptides; the number of unique peptides, and the biological process in which it is involved. Proteins that were also detected as intra-genotype DAPs are reported in italics.", "rows": [["UniProt Acc. No.", "Gene Code", "Organism", "Protein Description", "Growing Season 2010/2011", "Growing Season 2011/2012", "Intra-Genotype DAPs *", "Biological Process"], ["Fold Change", "p-Value", "Significance", "Peptides", "Unique Peptides", "Fold Change", "p-Value", "Significance", "Peptides", "Unique Peptides"], ["Russello vs. Simeto", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""], ["Q2A783", "AVLB1", "Wheat", "Avenin-like b1", "0.12", "4.84 × 10−11", "69.40", "7", "6", "0.12", "3.03 × 10−8", "109.29", "7", "6", "", "Storage"], ["B4FFZ9", "OBP1A", "Maize", "Oil body-associated protein 1A", "4.75", "7.00 × 10−5", "64.98", "5", "5", "9.73", "3.64 × 10−14", "88.47", "4", "4", "", "Others"], ["Q9ST58", "SPZ1C", "Wheat", "Serpin-Z1C", "0.40", "1.55 × 10−7", "48.73", "12", "5", "0.21", "1.09 × 10−8", "105.97", "11", "3", "Y (Russello)", "Defense/Inhibitor"], ["Timilia vs. Simeto", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""], ["P23951", "CHI2", "Barley", "26 kDa endochitinase 2", "0.44", "9.95 × 10−9", "79.42", "12", "7", "0.41", "3.01 × 10−5", "61.90", "12", "6", "", "Defense/Stress Related Proteins"], ["P01083", "IAA2", "Wheat", "α-amylase inhibitor 0.28", "64.00", "3.55 × 10−15", "68.66", "4", "3", "64.00", "1.13 × 10−10", "101.12", "6", "5", "", "Defense/Inhibitor"], ["P33044", "THHR", "Barley", "Antifungal protein R (Fragment)", "0.27", "4.72 × 10−18", "101.88", "2", "2", "0.32", "8.77 × 10−7", "69.64", "2", "2", "", "Defense/Stress Related Proteins"], ["Q2A783", "AVLB1", "Wheat", "Avenin-like b1", "3.33", "3.82 × 10−9", "95.07", "21", "21", "2.50", "7.97 × 10−6", "55.45", "21", "21", "Y (Timilia)", "Storage"], ["Q9FE01", "APX2", "Rice", "L-ascorbate peroxidase 2 cytosolic", "5.15", "4.43 × 10−8", "87.16", "2", "2", "2.32", "2.13 × 10−5", "51.24", "2", "2", "Y (Timilia)", "Defense/Stress Related Proteins"], ["B4FFZ9", "OBP1A", "Maize", "Oil body-associated protein 1A", "4.60", "4.17 × 10−9", "97.23", "5", "5", "9.09", "5.73 × 10−9", "106.51", "4", "4", "", "Others"], ["P82977", "ICIW", "Wheat", "Subtilisin-chymotrypsin inhibitor WSCI", "6.61", "7.87 × 10−9", "36.55", "2", "2", "4.67", "6.87 × 10−8", "84.71", "3", "3", "", "Defense/Inhibitor"], ["P31922", "SUS1", "Barley", "Sucrose synthase 1", "6.31", "1.37 × 10−7", "94.78", "10", "2", "3.95", "9.51 × 10−7", "51.48", "11", "3", "", "Starch biosynthesis"], ["Q43009", "SUS3", "Rice", "Sucrosesynthase 3", "3.13", "3.21 × 10−7", "77.26", "7", "2", "2.10", "9.56 × 10−5", "42.12", "10", "2", "", "Starch biosynthesis"], ["Timilia vs. Russello", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""], ["P23951", "CHI2", "Barley", "26 kD aendochitinase 2", "0.27", "3.29 × 10−4", "53.12", "17", "10", "0.33", "4.27 × 10−8", "87.68", "12", "6", "", "Defense/Stress Related Proteins"], ["P10846", "IAA3", "Wheat", "α-amylase inhibitor WDAI-3 (Fragment)", "0.39", "1.45 × 10−3", "36.20", "9", "4", "0.39", "3.91 × 10−6", "33.03", "8", "3", "Y (Timilia)", "Defense/Inhibitor"], ["Q2A783", "AVLB1", "Wheat", "Avenin-like b1", "38.49", "2.37 × 10−11", "99.23", "8", "6", "25.39", "1.84 × 10−8", "119.91", "8", "6", "Y (Timilia)", "Storage"], ["P29114", "LOX1", "Barley", "Linoleate 9S-lipoxygenase 1", "2.42", "1.31 × 10−6", "42.63", "8", "8", "2.28", "2.30 × 10−6", "55.34", "9", "9", "", "Others"], ["Q9ST57", "SPZ2A", "Wheat", "Serpin-Z2A", "0.02", "4.04 × 10−6", "96.72", "7", "3", "0.02", "3.47 × 10−13", "94.42", "5", "2", "", "Defense/Inhibitor"], ["P82977", "ICIW", "Wheat", "Subtilisin-chymotrypsin inhibitor WSCI", "6.74", "4.00 × 10−9", "79.02", "2", "2", "5.81", "2.35 × 10−8", "96.24", "3", "3", "", "Defense/Inhibitor"], ["P31922", "SUS1", "Barley", "Sucrose synthase 1", "3.36", "3.11 × 10−7", "68.34", "13", "3", "2.05", "2.74 × 10−5", "45.72", "12", "4", "", "Starch biosynthesis"], ["Q43009", "SUS3", "Rice", "Sucrose synthase 3", "3.11", "6.36 × 10−7", "58.15", "7", "2", "2.30", "1.03 × 10−5", "50.21", "7", "2", "", "Starch biosynthesis"]], "row_count": 25, "column_count": 16, "numeric_cells": 232, "header_rows": 2, "locator": "section[3]/table-wrap[2]#molecules-26-02596-t002"}}, {"id": "asset:table:pmid:33946829:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:fe370c899ca10be93190909f500e57eee8870a12c32c3ea0f3ba03760d2627a8", "bytes": 761, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#array1", "version": null, "note": null, "structure": {"pmcid": "PMC8124627", "section_index": 13, "section_title": "Abbreviations", "row_count": 19, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["MS", "Mass Spectrometry"], ["CD", "Celiac Deasease"], ["IgE", "Immunoglobulin E"], ["NCWS", "Non Celiac Wheat Sentivity"], ["DAP", "Differentially Abundant Proteins"], ["WSCI", "Subtilisin Chymotrypsin Inhibitor"], ["ALPs", "Avenin-Like Proteins"], ["SUS1", "Sucrose Synthase 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"verbatim", "quote": "A protein was quantified when: (i) at least two of its unique peptides satisfied the parameters above reported; (ii) was identified in a minimum of five out of nine nanoLC-MS/MS runs per flour sample; and (iii) had a p-value < 0.05 and a significance ≥ 20 (significance method ANOVA; the significance score was calculated as the −10log10 of the significance testing p-value)."}}, {"id": "method-2", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "hierarchical clustering"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD024204"], "resolved_accessions": ["PXD024204"], "statements": ["Not applicable."], "basis": "The paper names PXD024204 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. 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