| Literature DB >> 35252491 |
Liliana Anjos1, Patrícia I S Pinto1, Soraia Santos1, M Dulce Estêvão1,2, Cátia Santa3,4, Bruno Manadas3,4, Adelino V M Canário1,5, Deborah M Power1,5.
Abstract
Contamination of aquatic ecosystems with anthropogenic pollutants, including pharmaceutical drugs, is a major concern worldwide. Aquatic organisms such as fish are particularly at risk of exposure to pollutants. The surface of fish is the first point of contact with pollutants, but few studies have considered the impact of pollutants on the skin-scale barrier. The present proteome data are the basis of the findings discussed in the associated research article "Proteomics of sea bass skin-scales exposed to the emerging pollutant fluoxetine compared to estradiol" [1]. Juvenile sea bass were exposed by intraperitoneal injections to: a) the antidepressant fluoxetine (FLX), a widely prescribed psychotropic drug and an emerging pollutant; b) the natural estrogen 17β-estradiol (E2) and c) the vehicle, coconut oil (control). The scale proteome of fish exposed to these compounds for 5 days was analysed using quantitative label-free proteomics technology SWATH-MS (sequential windowed data-independent acquisition of the total high-resolution-mass spectra). The proteome data generated was submitted to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD020983. LC-MS data from pooled protein extracts from the scales of all experimental groups was acquired using information-dependent acquisition (IDA) and 1,254 proteins were identified by searching against the sea bass genome database. 715 proteins were quantified by SWATH acquisition, and 213 proteins had modified levels (p < 0.05) between the E2- or FLX-exposed fish compared to the control. The main biological processes and KEGG pathways affected by E2 or FLX treatments were identified using Cytoscape/ClueGO enrichment analyses.Entities:
Keywords: Antidepressant; Emerging pollutants; Estrogen; SWATH-MS quantitative proteomics; Scales
Year: 2022 PMID: 35252491 PMCID: PMC8889360 DOI: 10.1016/j.dib.2022.107971
Source DB: PubMed Journal: Data Brief ISSN: 2352-3409
The number of proteins and peptides in the SWATH proteomic analysis obtained from the sea bass protein extracts of scales from treated and/or control animals. The number of identified proteins/peptides is shown for each of the two individual libraries generated (IDA analysis): “Pooled C_library” (prepared from pools of control samples) and for the global identification library “Pooled C, E2, FLX_library”, that was generated by combining all the files obtained from the 3 independent pools of each experimental condition and was used as the library for SWATH quantification. The number of identified/quantified proteins obtained by SWATH processing under confident quantitative values (local FDR < 0.05, p < 0.05) and the number of proteins with modified levels due to E2 of FLX treatments (p < 0.05) are presented, as well as the corresponding Tables where detailed results can be found.
| N° of Proteins | N° of Peptides | Supported by ≥ 3 peptides (95%) | Table link | |
|---|---|---|---|---|
| Pooled C_library | 985 | 5710 | 560 | Supp. Table 1_worksheet-ProteinSummary |
| Pooled C, E2, FLX_library | 1254 | 8073 | 728 | Supp. Table 3_worksheet-ProteinSummary |
| 715 | − | − | Supp. Table 4_worksheet-Proteins_ITotal | |
| 213 | − | − | Supp. Table 4 and Table S4 in the research manuscript | |
| 110 | − | − | Supp. Table 4 and Table S4 in the research manuscript | |
| Up | 89 | − | − | Supp. Table 4 and Table S4 in the research manuscript |
| Down | 21 | − | − | Supp. Table 4 and Table S4 in the research manuscript |
| 134 | − | − | Supp. Table 4 and Table S4 in the research manuscript | |
| Up | 55 | − | − | Supp. Table 4 and Table S4 in the research manuscript |
| Down | 79 | − | − | Supp. Table 4 and Table S4 in the research manuscript |
| 31 | − | − | Supp. Table 4 and Table S4 in the research manuscript | |
| 79 | − | − | Supp. Table 4 and Table S4 in the research manuscript | |
| 103 | − | − | Supp. Table 4 and Table S4 in the research manuscript | |
Figure 1Functional enrichment analyses of all proteins identified in protein extracts of sea bass scales (control samples). The enriched Gene Ontology Biological Processes (GO-BP) that were overrepresented in the global sea bass scale proteome are identified (see Suppl. Table 1 for the list of identified proteins). Enrichment for GO terms was carried out using the ClueGO plugin and Cytoscape software, which found 562 terms with significant enrichment (FDR < 0.05). Represented are 55 functional groups with significant enrichment (FDR < 0.05) that clustered the 562 significant GO terms according to their functional classification. For detailed lists of all significantly enriched GO terms and groups and associated KEGG pathways consult Suppl. Table 2. The length of bars represents the significance of each group in the ClueGO network output measured by the enrichment score (−log2 (group FDR)).
Figure 2Number of proteins in the sea bass scale proteome with a differential expression in response to estradiol or fluoxetine exposure. The Venn diagram shows the number of proteins with significantly different levels between the control scales and scales exposed to estradiol (E2) or to fluoxetine (FLX) for 5 days (FDR < 0.05). The pie charts correspond to the total number of proteins affected by E2 (110) or by FLX (134). The percentage of proteins that increased are shown in red and the percentage of proteins that decreased are shown in green. The size of the circles in the Venn diagram and pie charts is proportional to the number of proteins with modified expression in each treatment compared to the control.
| Subject | Molecular Biology |
| Specific subject area | Ecotoxicology, Endocrine disruption, Environment, Pollution. |
| Type of data | Table, figures, supplementary tables. |
| How data were acquired | Triple TOF 5600 (ABSciex) LC (nanoLC Ultra 2D, Eksigent)-SWATH-MS system with information-dependent acquisition (IDA). |
| Data format | Raw |
| Parameters for data collection | Marine cultured sea bass were exposed to estradiol and fluoxetine by intraperitoneal injection and 5 days later the scales and adhering epithelia were collected. |
| Description of data collection | Protein extraction, protein quantification and quality evaluation, short-GeLC-SWATH-MS proteome library preparation, protein identification and quantification, statistical analyses and bioinformatics analyses. |
| Data source location | Centro de Ciências do Mar (CCMAR), Faro, Algarve, Portugal (37° 1′ 0″ N; 7° 56′ 0″ W). |
| Data accessibility | Within the present article and deposited in the PRIDE repository (ProteomeXchange Consortium). |
| Related research article | P.I. Pinto, L. Anjos, M. Estêvão, S. Santos, C. Santa, B. Manadas, T. Monsinjon, A.V.M. Canário, D.M. Power, Proteomics of sea bass skin-scales exposed to the emerging pollutant fluoxetine compared to estradiol, Science of The Total Environment (2021) 152671 |