{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD029865/JPeragon_sol26-17_C2_19072017.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD029865/JPeragon_sol26-17_C3_19072017.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD029865/JPeragon_sol26-17_EO3_19072017.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD029865/JPeragon_sol26-17_C1_19072017.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD029865/JPeragon_sol26-17_EO2_19072017.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD029865/JPeragon_sol26-17_EO1_19072017.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD029865/txt.rar"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"labhead_mail":["jperagon@ujaen.es"],"submitter":["Carlos Alberto Fuentes Almagro"],"technology_type":["Mass Spectrometry","Shotgun proteomics"],"software":[""],"submitter_keywords":["Nadph","Antioxidant enzymes","Ros","Hepg2","Proteome","Cytotoxicity","Erythrodiol","Gsh"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD029865"],"tissue":["Hepatocyte","Cell Culture"],"sample_protocol":["To prepare the samples, cells at 70% confluence were incubated with IC50 concentration of EO for 24 h. They were then washed three times with PBS, scraped off with a cell scraper (Renner), and put into 0.5 mL of lysis buffer containing 8 M urea, 2 M thiourea, 4% CHAPS, 2% IPG buffer, 20 mM dithiothreitol (DTT), 100 mM HCl-Tris, 0.75 mM phenylmethylsulfonyl fluoride (PMSF) (pH 8). These samples before being immediately sonicated on ice for 5 min and shaken gently for 1 h at 4°C. During this time, the samples were moderately shaken in a vortex every 15 minutes. Lysates were centrifuged at 10,000xg for 15 min at 4°C. The supernatants were used for nLC-MS proteomics procedure. Three replicates were prepared for each experimental group, each being made up of 3 different populations of cells.  The nLC-MS proteomics approach was applied as described in Cuevas-Fernández et al., (2019). Briefly, the samples were cleaned by 1D electrophoresis, subsequently digested with trypsin on polyacrylamide gel to remove possible contaminants, and dried in a speedvac. The dried peptides were resuspended in 2% acetonitrile (ACN) and 0.05% trifluoroacetic acid (TFA), and 400 ng of each was injected for analysis. nLC-MS was performed on a Dionex Ultimate 3000 nLC (Thermo Scientific) with a flow of 300 nL/min and an ACN gradient from 3 to 40% in 60 min in 0.1% formic acid (FA). The peptides were first trapped in a 5 mm × 300 um Acclaim Pepmap precolumn and subsequently separated on a 50 cm × 75 µm Acclaim Pepmap nano-column (Thermo Scientific) with a 2 µm particle size. Eluted peptides were analyzed on an Orbitrap Fusion mass spectrometer (Thermo Scientific) equipped with a nanoelectrospray source. A data dependent acquisition method was applied, first detecting the peptides in the Orbitrap detector at 120,000 resolution, followed by collision-induced dissociation (CID) fragmentation in the ion trap to obtain the MS2 spectra."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Peptide identification and quantitation were processed using the MaxQuant package (version 1.6.3.4). Peptide identification was carried out with the Andromeda engine against a database of Uniprot Homo sapiens (July 2017) (www.uniprot.org) applying default settings using MaxQuant software, in a MaxLFQ label-free quantification method (Cox and Mann, 2008; Cox et al., 2014). MaxQuant software enables high peptide identification rates, individualized ppb range mass accuracy and proteome-wide protein quantification (Cox and Mann, 2008). MS2 spectra were searched. Briefly, peptides were generated from tryptic digestion with up to one missed cleavage, carbamidomethylation of cysteines as a fixed modification, and oxidation of methionine as a variable modification. Precursor mass tolerance was 10 ppm and product ions were searched for at 0.6 Da tolerance. Valid peptides were filtered according to the 1% false discovery rate (FDR) q-value. A target-decoy search method was applied, integrating multiple peptide parameters such as length, charge, number of modifications, and identification score in a single quality acting as statistical evidence of the quality of each spectrum match of peptides. Peptide quantification was performed with the MaxLFQ label-free method. A retention time alignment and identification transfer protocol (“match-between-runs” feature in MaxQuant) was applied. Proteins identified from at least 2 peptides were considered in this analysis. Measurement of normalized label-free quantitation (LFQ) intensities obtained with MaxQuant was conducted on the Perseus software platform (https://maxquant.net/perseus/) (Tyanova et al., 2016). Peak intensities across the whole set of quantitative data for all peptides in the samples were imported from the LFQ intensities of proteins from the MaxQuant analysis and normalized according to the median. LFQ normalized intensity values were transformed to a base 2 logarithmic scale. Proteins identified in at least 2 replicates were considered. Imputation values with the value of the lowest intensity for missing data were applied in a maximum of one replicate per condition (imputed). Protein quantification and calculation of statistical significance were carried out using two-way Student’s t-test and error correction (adjusted p-value) was performed with the Benjamini–Hochberg method. Results obtained were then filtered, and adjusted p value ≤ 0.05 and fold change ≥ 2 were considered."],"omics_type":["Proteomics"],"labhead":["Juan Peragon Sanchez"],"instrument_platform":[""],"labhead_affiliation":["Biochemistry and Molecular Biology Area Departament of Experimental biology University of Jaen (Spain) Campus Las Lagunillas, B3-356 23071, Jaén, Tel.: 953212523"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"publication":["35052578 Peñas-Fuentes JL, Siles E, Rufino-Palomares EE, Pérez-Jiménez A, Reyes-Zurita FJ, Lupiáñez JA, Fuentes-Almagro C, Peragón-Sánchez J. Effects of Erythrodiol on the Antioxidant Response and Proteome of HepG2 Cells. Antioxidants (Basel). 2021 11(1) 10.3390/antiox11010073"],"submitter_mail":["b72fualc@gmail.com"],"submitter_affiliation":["University of Cordoba"],"submitter_country":["Spain"],"pubmed_abstract":["Erythrodiol (EO) is a pentacyclic triterpenic alcohol found in olive tree leaves and olive oil, and it has important effects on the health properties and quality of olive oil. In this study, we characterized the cytotoxic effects of EO on human hepatocarcinoma (HepG2) cells by studying changes in cell viability, reactive oxygen species (ROS) production, antioxidant defense systems, and the proteome. The results reveal that EO markedly decreased HepG2 cell viability without changing ROS levels. The concentrations of glutathione and NADPH were significantly reduced, with selective changes in the activity of several antioxidant enzymes: glutathione peroxidase, glutathione reductase, glucose 6-phosphate dehydrogenase, and 6-phosphogluconate dehydrogenase. Proteomic data reveal that EO led to the complete elimination or decreased abundance of 41 and 3 proteins, respectively, and the abundance of 29 proteins increased. The results of functional enrichment analysis show that important metabolic processes and the nuclear transport of mature mRNA were impaired, whereas AMP biosynthesis and cell cycle G2/M phase transition were induced. The transcription factors and miRNAs involved in this response were also identified. These potent antiproliferative effects make EO a good candidate for the further analysis of its hepatic antitumor effects in in vivo studies."],"pubmed_title":["Effects of Erythrodiol on the Antioxidant Response and Proteome of HepG2 Cells."],"pubmed_authors":["Peñas-Fuentes Juan Luis JL, Siles Eva E, Rufino-Palomares Eva E EE, Pérez-Jiménez Amalia A, Reyes-Zurita Fernando J FJ, Lupiáñez José A JA, Fuentes-Almagro Carlos C, Peragón-Sánchez Juan J"],"additional_accession":[]},"is_claimable":false,"name":"EFFECTS OF ERYTHRODIOL ON THE ANTIOXIDANT RESPONSE AND PROTEOME OF HepG2 CELLS","description":"Erythrodiol (EO) is a pentacyclic triterpenic alcohol found in the leaf of olive tree and in the olive oil. In this study, we evaluate the nature of cytotoxicity of EO on HepG2 hepatocarcinoma human cells studying the changes induced on cell viability, reactive oxygen species (ROS) production, antioxidant defence systems and proteome. The results obtained reveal that EO markedly decrease HepG2 cell viability without change ROS levels. A significant reduction in the glutathione and NADPH concentrations are produced with selective changes in the activity of antioxidant enzymes (glutathione peroxidase, glutathione reductase, glucose 6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase). Proteomics data reveals that 41 and 3 proteins are decreased completely or partially in abundance, respectively; and 29 are completely increased. The functional enrichment analysis showed that an impairment of important metabolic processes and in the nuclear transport of mature mRNA is produced while the biosynthesis of AMP and cell cycle G2/M phase transition are induced. The transcription factors and miRNA implied in this response are also 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