Time-course investigation of Phytophthora infestans infection of potato leaf from three cultivars by quantitative proteomics.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26862565", "kind": "science-record", "revision": 3, "content_hash": "sha256:fb7ab4e0fd5ccc016446f23d6957ed9df80db6698f8d0d80c4920114431a235b", "created_at": "2026-11-01T15:40:15Z", "updated_at": "2026-11-01T18:47:57Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Time-course investigation of Phytophthora infestans infection of potato leaf from three cultivars by quantitative proteomics.", "doi": "10.1016/j.dib.2015.11.069", "pmid": "26862565", "authors": ["Mia Kruse Guldstrand Larsen", "Malene Møller Jørgensen", "Tue Bjerg Bennike", "Allan Stensballe"], "journal": "Data in brief", "year": 2016, "abstract": "Potato late blight is one the most important crop diseases worldwide. Even though potato has been studied for many years, the potato disease late blight still has a vast negative effect on the potato production [1], [2], [3]. Late blight is caused by the pathogen Phytophthora infestans (P. infestans), which initiates infection through leaves. However, the biological activities during different stages of infection are poorly described, and could enable novel or improved ways of defeating late blight infection [4]. Therefore, we investigated the interactions between P. infestans (mixed strain culture) and potato (Solanum tuberosum). Three commercially available field potato cultivars of different resistance to late blight infection; Kuras (moderate), Sarpo Mira (highly resistant) and Bintje (very susceptable) were grown under controlled green house conditions and inoculated with a diversity of P. infestans populations. We used label-free quantitative proteomics to investigate the infection with P. infestans in a time-course study over 258 h. Several key issues limits proteome analysis of potato leaf tissue [5], [6], [7]. Firstly, the immense complexity of the plant proteome, which is further complicated by the presence of highly abundant proteins, such as ribulose bisphosphate carboxylase/oxygenase (RuBisCO). Secondly, plant leaf and potato, in particular, contain abundant levels amounts of phenols and polyphenols, which hinder or completely prevent a successful protein extraction. Hitherto, protein profiling of potato leaf tissues have been limited to few proteome studies and only 1484 proteins have been extracted and comprehensively described [5], [8], [9]. We here present the detailed methods and raw data by optimized gel-enhanced label free quantitative approach. The methodology enabled us to detect and quantify between 3248 and 3529 unique proteins from each cultivar, and up to 758 P. infestans derived proteins. The complete dataset is available via ProteomeXchange, with the identifier PXD002767.", "claims": [{"id": "claim-data-access", "statement": "The proteomics raw data and MaxQuant result-files from the analysis have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD0002767 [11], [12], [13], [14], and can be downloaded directly (http://www.ebi.ac.uk/pride/archive/projects/PXD002767).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26862565", "locator": "sections[10] \"Data\" paragraph 2", "quote": "The proteomics raw data and MaxQuant result-files from the analysis have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD0002767 [11], [12], [13], [14], and can be downloaded directly (http://www.ebi.ac.uk/pride/archive/projects/PXD002767)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used MaxQuant-based label-free quantitative proteomics, with statistical analysis based on the search-output files deposited in the ProteomeXchange/PRIDE repository under dataset identifier PXD002767; the methodology detected and quantified 3,248–3,529 unique proteins per cultivar and up to 758 P. infestans-derived proteins.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26862565", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The methodology enabled us to detect and quantify between 3248 and 3529 unique proteins from each cultivar, and up to 758 P. infestans derived proteins."}, {"asset": "source:pmid:26862565", "locator": "sections[9] \"Proteomic data analysis\" paragraph 2", "quote": "This enables statistical analysis based on the search output files as provided in the ProteomXchange and described in detail in Table 2."}, {"asset": "source:pmid:26862565", "locator": "sections[10] \"Data\" paragraph 2", "quote": "The proteomics raw data and MaxQuant result-files from the analysis have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD0002767 [11], [12], [13], [14], and can be downloaded directly (http://www.ebi.ac.uk/pride/archive/projects/PXD002767)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used MaxQuant-based label-free quantitative proteomics, with statistical analysis based on the search-output files deposited in the ProteomeXchange/PRIDE repository under dataset identifier PXD002767; the methodology detected and quantified 3,248–3,529 unique proteins per cultivar and up to 758 P. infestans-derived proteins.", "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:26862565"], "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:PXD002767"], "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:PXD002767"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26862565", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2015.11.069", "sha256": "sha256:fdf4efdf317785fff6a00e095479ee872cb24c0ff6ee3b09a3161f9ecad92e08", "bytes": 19654, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2015.11.069", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4707178", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD002767", "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=PXD002767", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD002767", "version": null, "note": "The proteomics raw data and MaxQuant result-files from the analysis have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD0002767 [11], [12], [13], [14], and can be downloaded directly (http://www.ebi.ac.uk/pride/archive/projects/PXD002767).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The proteomics raw data and MaxQuant result-files from the analysis have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD0002767 [11], [12], [13], [14], and can be downloaded directly (http://www.ebi.ac.uk/pride/archive/projects/PXD002767).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Time-course Investigation of Phytophthora infestans infection of potato leaf from three cultivars by quantitative proteomics", "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:26862565:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:563a13bad1d72b94bc95f7ddc3d8c223f8a9910fcf95c3011041d9b9ecfa502b", "bytes": 1839, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#t0005", "version": null, "note": "Description of search file-names in the ProteomeXchange repository PXD002767 based on MaxQuant [11]. Each zip contains a range of files where the four most relevant are described above.", "structure": {"pmcid": "PMC4707178", "section_index": 9, "section_title": "Proteomic data analysis", "row_count": 9, "column_count": 2}, "table": {"label": "Table 2", "caption": "Description of search file-names in the ProteomeXchange repository PXD002767 based on MaxQuant [11]. Each zip contains a range of files where the four most relevant are described above.", "rows": [["Search Files Filename", "Description of content"], ["MQ_Search_Kuras.zip", "MaxQuant result folder “txt” of Q Exactive GelMS potato leaf samples, search against the Uniprot reference proteome databases for potato (AUP000011115) and late blight (AUP000006643)."], ["MQ_Search_Bintje.zip", "MaxQuant result folder “txt” of Q Exactive GelMS potato leaf samples, search against the Uniprot reference proteome databases for potato (AUP000011115) and late blight (AUP000006643)."], ["MQ_Search_Sarpomira.zip", "MaxQuant result folder “txt” of Q Exactive GelMS potato leaf samples, search against the Uniprot reference proteome databases for potato (AUP000011115) and late blight (AUP000006643)."], ["MQ_Search_all_cultivars.zip", "MaxQuant result folder “txt” of Q Exactive GelMS potato leaf samples from all cultivars, search against the Uniprot reference proteome databases for potato (AUP000011115) and late blight (AUP000006643)."], ["The MaxQuant output in folder \"txt\" contains a range of files containing important search information. Below files are the most commonly used for post-identification analysis and quantitative analysis."], ["tables.pdf", "A summary of all the definitions and files used for the MaxQuant search."], ["proteinGroups.txt", "File containing all proteins with corresponding label free quantitative information to be imported into the Perseus post-analysis program [15]."], ["summary.txt parameters.txt", "Detailed description of all settings used for the MaxQuant search."]], "row_count": 9, "column_count": 2, "numeric_cells": 5, "header_rows": 1, "locator": "section[9]/table-wrap[1]#t0005"}}, {"id": "asset:table:pmid:26862565:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0cfaa28c3553a0bc88987b90c196de51066f8ed1976e32d33c6934dcea11f4fc", "bytes": 9093, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#t0010", "version": null, "note": "Description of file-names in the ProteomeXchange repository PXD002767. MS files were searched using using MaxQuant [10]. Combining fractions of GelMS (1top-4bottom) gel lanes. The number of identified proteins after filtration of typical contaminants and Phytophthora infestans is reported.", "structure": {"pmcid": "PMC4707178", "section_index": 10, "section_title": "Data", "row_count": 309, "column_count": 6}, "table": {"label": "Table 1", "caption": "Description of file-names in the ProteomeXchange repository PXD002767. MS files were searched using using MaxQuant [10]. Combining fractions of GelMS (1top-4bottom) gel lanes. 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