Proteome dataset of chili pepper plant (Capsicum frutescens) infested by broad mite (Polyphagotarsonemus latus).

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34041315", "kind": "science-record", "revision": 5, "content_hash": "sha256:7e7102535edef35e72f9b8b9660000d9be3856b9dc5cd91f0065b7aabc3b5c67", "created_at": "2026-11-01T15:41:36Z", "updated_at": "2026-11-01T22:03:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteome dataset of chili pepper plant (Capsicum frutescens) infested by broad mite (Polyphagotarsonemus latus).", "doi": "10.1016/j.dib.2021.107095", "pmid": "34041315", "authors": ["Sachin S Patavardhan", "Kriti Awasthi", "Suhasini Suresh", "Pratigya Subba", "Mohd Altaf Najar", "Leo D'Souza", "Shashi Kiran Nivas", "Thottethodi Subrahmanya Keshava Prasad"], "journal": "Data in brief", "year": 2021, "abstract": "The dataset presented in this article is associated with the TMT (Tandem mass tag) labeled proteomics of chili pepper plant (Capsicum frutescens) infested by a broad mite (Polyphagotarsonemus latus). Data was captured using a nano liquid chromatography system coupled with high-resolution Orbitrap FusionTribridmass spectrometer. Proteomics data was analyzed using the Proteome Discoverer version 2.4 tool using MASCOT and SequestHT algorithms. We have identified a total of 5,807 proteins supported by 48,555 unique peptides and 1,279,655 peptide-spectrum matches. Individually, 5,186 proteins were detected in healthy leaf samples, 5,193 in infested leaf sample, 5,194 proteins in healthy meristem sample, and 5,196 proteins in infested meristem samples. Datasets obtained from reciprocal blast against the Arabidopsis thaliana proteome database enabled the prediction of protein-protein interactions, and subcellular localization of differentially expressed proteins, which are also included in this article. Data presented in this article has been deposited in the ProteomeXchange Consortium via the PRIDE repository, which can be accessed through the accession ID: PXD018653.", "claims": [{"id": "claim-data-access", "statement": "The mass spectrometry raw data and the Proteome Discoverer output MSF files obtained from this study are publically available at ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) through the PRIDE partner repository (Project accession: PXD018653).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34041315", "locator": "sections[11] \"Data availability\" paragraph 2", "quote": "The mass spectrometry raw data and the Proteome Discoverer output MSF files obtained from this study are publically available at ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) through the PRIDE partner repository (Project accession: PXD018653)."}], "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:34041315"], "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:PXD018653"], "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:PXD018653"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34041315", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2021.107095", "sha256": "sha256:cf03f90cc24fedff26a39ee8ff8dca311a2167faa8d8bd3410862d262e8e00a8", "bytes": 20250, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2021.107095", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8142047", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD018653", "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=PXD018653", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD018653", "version": null, "note": "The mass spectrometry raw data and the Proteome Discoverer output MSF files obtained from this study are publically available at ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) through the PRIDE partner repository (Project accession: PXD018653).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry raw data and the Proteome Discoverer output MSF files obtained from this study are publically available at ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) through the PRIDE partner repository (Project accession: PXD018653).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Capsicum leaf and meristem LC-MS/MS", "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:34041315:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:74feb118a8e3d51863de205c070d4546e1c2d645f1249e88386c2ffb7bb26d95", "bytes": 2461, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#utbl0001", "version": null, "note": null, "structure": {"pmcid": "PMC8142047", "section_index": 1, "section_title": "Specifications Table", "row_count": 10, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject", "Plant Science"], ["Specific subject area", "Plant–insect interaction"], ["Type of data", "TableFigure"], ["How data were acquired", "Thermo Scientific Orbitrap Fusion Tribrid mass spectrometer (Thermo Fischer Scientific, Bremen, Germany)Proteome Discoverer 2.4with SequestHT and MASCOT (Matrix Science,London, UK; version 2.2)"], ["Data format", "Analyzed"], ["Parameters for data collection", "Sample collection was carried out from a broad mite-infested field. Plants grew at an ambient temperature of 27 °C with a relative humidity of 65–85%. Meristem and leaf samples of 12-weeks-old healthy and infected plants were collected for the proteomics analysis."], ["Description of data collection", "The plant sample was homogenized using liquid nitrogen, proteins were extracted, disulphide bonds were reduced and alkylated. Proteins were subjected to trypsin digestion. Peptides were ladled with tandem mass tags (TMT) and fractionated using basic reverse-phase liquid chromatography (bRPLC). Peptide fractions were subjected to high-resolution mass spectrometry analysis to obtain peptide sequence information. Data was searched against Capsicum annuum (Pepper Zunla 1 Ref_v1.0) protein database to fetch peptide spectrum matches, from which a list of corresponding peptides and proteins were obtained. Identified proteins were subjected to bioinformatic analysis."], ["Data source location", "Institution: St Aloysius College (Autonomous)City/Town/Region: Mangaluru, Karnataka stateCountry: IndiaLatitude and longitude for collected samples/data:12°52′26.3″N 74°50′45.9″E, 28 September 2018"], ["Data accessibility", "Repository name: ProteomeXchangeData identification number: PXD018653Direct URL to data: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/08/PXD018653Orhttp://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD018653Supplementary files can be accessed from: https://data.mendeley.com; DOI: http://dx.doi.org/10.17632/5j93jhjh6n.1"], ["Related research article", "Patavardhan, S. S., Subba, P., Najar, A., Awasthi, K., D'Souza, L., Prasad, T. S. K. and Nivas, S. K., 2020. Plant–Pathogen Interactions: Broad Mite (Polyphagotarsonemuslatus)-Induced Proteomic Changes in Chili Pepper Plant (Capsicum frutescens). OMICS: A Journal of Integrative Biology, 24(12), 714–725."]], "row_count": 10, "column_count": 2, "numeric_cells": 6, "header_rows": 0, "locator": "section[1]/table-wrap[1]#utbl0001"}}, {"id": "asset:table:pmid:34041315:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:df08b4a6585741478c1f64fcd68d090855e50df92e502c7d6ab4535800560620", "bytes": 2188, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#tbl0001", "version": null, "note": "Partial list of proteins identified in Capsicum frutescens leaf and meristem associated with plant-pathogen interaction as annotated by KEGG pathways.", "structure": {"pmcid": "PMC8142047", "section_index": 3, "section_title": "Data Description", "row_count": 26, "column_count": 4}, "table": {"label": "Table 1", "caption": "Partial list of proteins identified in Capsicum frutescens leaf and meristem associated with plant-pathogen interaction as annotated by KEGG pathways.", "rows": [["Protein accession", "Name of the protein", "Fold change in leaf", "Fold change in meristem"], ["XP_016537868.1", "3-ketoacyl-coa synthase 10", "1.12", "0.45"], ["XP_016538117.1", "Mitogen-activated protein kinase homolog MMK2", "1.88", "1.37"], ["XP_016539393.1", "Basic form of pathogenesis-related protein 1-like", "4.44", "4.01"], ["XP_016543739.1", "Probable calcium-binding protein CML49", "2.66", "0.93"], ["XP_016547276.1", "Heat shock protein 90–5, chloroplastic", "1.56", "1.17"], ["XP_016547536.1", "Calmodulin-like", "2.95", "0.88"], ["XP_016547769.1", "Probable calcium-binding protein CML48", "2.05", "0.76"], ["XP_016551150.1", "PTI1-like tyrosine-protein kinase 1 isoform X1", "1.68", "0.92"], ["XP_016551464.1", "RPM1-interacting protein 4-like isoform X1", "1.99", "0.93"], ["XP_016554291.1", "Calcium-dependent protein kinase SK5-like", "1.68", "1.13"], ["XP_016555153.1", "Probable disease resistance protein At1g61190", "3.92", "1.49"], ["XP_016555855.1", "Calcium-binding allergen Ole e 8-like", "1.76", "0.95"], ["XP_016562961.1", "Glycerol kinase", "1.58", "1.53"], ["XP_016567554.1", "Mitogen-activated protein kinase 6", "2.74", "0.59"], ["XP_016570057.1", "Calcium-dependent protein kinase 11-like", "1.71", "1.20"], ["XP_016578314.1", "Protein EDS1-like", "2.47", "1.25"], ["XP_016580574.1", "Chitin elicitor receptor kinase 1-like isoform X1", "3.30", "1.44"], ["XP_016573586.1", "Pto-interacting protein 1-like", "1.53", "0.99"], ["XP_016541443.1", "Pathogenesis-related leaf protein 4-like", "0.43", "0.65"], ["XP_016547427.1", "Mitogen-activated protein kinase homolog NTF4", "0.47", "1.16"], ["XP_016564510.1", "Heat shock protein 83-like", "0.64", "1.31"], ["XP_016565607.1", "Elongation factor Tu, mitochondrial", "0.65", "0.86"], ["XP_016565630.1", "Calcium-dependent protein kinase 4", "0.59", "1.04"], ["XP_016572842.1", "Caltractin-like isoform X1", "0.65", "0.91"], ["XP_016580498.1", "Heat shock protein 90–6, mitochondrial", "0.55", "0.96"]], "row_count": 26, "column_count": 4, "numeric_cells": 92, "header_rows": 1, "locator": "section[3]/table-wrap[1]#tbl0001"}}], "gaps": ["asset:data:geo:PXD018653 not downloaded", "asset:data:geo:PXD018653 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "sequence_alignment", "specific": "blast", "label": "Sequence alignment / homology", "dsl_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["sequence_records"], "evidence": {"score": 0.7, "band": "medium", "quote": "blast"}}], "targets": [], "gaps": []}, "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: blast."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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