Experimental data from flesh quality assessment and shelf life monitoring of high pressure processed European sea bass (Dicentrarchus labrax) fillets

Abstract

Fresh fish are highly perishable food products and their short shelf-life limits their commercial exploitation and leads to waste, which has a negative impact on aquaculture sustainability. New non-thermal food processing methods, such as high pressure (HP) processing, prolong shelf-life while assuring high food quality. The effect of HP processing (600MPa, 25 °C, 5min) on European sea bass (Dicentrarchus labrax) fillet quality and shelf life was investigated. The data presented comprises microbiome and proteome profiles of control and HP-processed sea bass fillets from 1 to 67 days of isothermal storage at 2 °C. Bacterial diversity was analysed by Illumina high-throughput sequencing of the 16S rRNA gene in pooled DNAs from control or HP-processed fillets after 1, 11 or 67 days and the raw reads were deposited in the NCBI-SRA database with accession number PRJNA517618. Yeast and fungi diversity were analysed by high-throughput sequencing of the internal transcribed spacer (ITS) region for control and HP-processed fillets at the end of storage (11 or 67 days, respectively) and have the SRA accession number PRJNA517779. Quantitative label-free proteomics profiles were analysed by SWATH-MS (Sequential Windowed data independent Acquisition of the Total High-resolution-Mass Spectra) in myofibrillar or sarcoplasmic enriched protein extracts pooled for control or HP-processed fillets after 1, 11 and 67 days of storage. Proteome data was deposited in the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD012737. These data support the findings reported in the associated manuscript “High pressure processing of European sea bass (Dicentrarchus labrax) fillets and tools for flesh quality and shelf life monitoring”, Tsironi et al., 2019, JFE 262:83–91, doi.org/10.1016/j.jfoodeng.2019.05.010.

Proteome dataset of sea bass (Dicentrarchus labrax) skin-scales exposed to fluoxetine and estradiol

“…Total protein was extracted from the previously collected sea bass frozen scales for SWATH-MS quantitative proteomics analysis. The methodology used was a modification of the method previously reported in Anjos and Tsironi [ 6 , 7 ]. In brief, frozen scales (30 - 60 mg of scales per fish) were resuspended in 1 ml of ice-cold protein extraction buffer (50 mM Tris buffer at pH 6.8, 100 mM DTT, 1.7 % SDS) in 13 ml plastic tubes (SARSTEDT; Germany).…”

“…Samples were analysed on a Triple TOF™ 5600 System (Sciex®, Framingham, MA) through two operative phases: Information-dependent acquisition (IDA) of the pooled samples (Pool control (C), Pool E2 and Pool FLX); and the subsequent SWATH acquisition of each replicate sample from the 3 experimental conditions (n = 7 individual replicates per experimental condition). Peptide separation was obtained by liquid chromatography (nanoLC Ultra 2D, Eksigent®, CA) and IDA experiments were performed following the methodology described in Anjos [6] with the exception that the LC linear gradient was 5 % to 30 % ACN in 0.1 % FA and the mass spectrometer was operated with Analyst® TF 1.6, ABSciex®. The same chromatographic conditions used for IDA acquisitions were maintained for SWATH-MS analysis.…”

“…The same chromatographic conditions used for IDA acquisitions were maintained for SWATH-MS analysis. The SWATH setup was based on Gillet [11] using the same parameters described in Anjos [6] with the exception that the survey scan acquired at the beginning of each cycle for instrument calibration was of 250 ms in between the 350 - 1500 m/z precursor range.…”

“…Data processing was carried out using the SWATH TM processing plug-in for PeakView TM (v2.0.01, ABSciex®) as described in Anjo [9] with minor modifications. Peptides were selected automatically from the C, E2, FLX pooled library as described in Anjos [6] and selection criteria included: i) unique peptides for a specific targeted protein were ranked by the intensity of the precursor ion from the IDA analysis; ii) peptides that contained biological modifications and/or were shared between different protein entries/isoforms were excluded. After retention time adjustment using the internal standard mal E-GFP peptides, up to 15 peptides, with up to 5 fragments each, were automatically selected per protein, and quantification was attempted for all proteins from the library that had a score in Protein Pilot below 5 % local FDR.…”

Proteomics of Fish White Muscle and Western Blotting to Detect Putative Allergens

“…Three main protein fractions can be extracted from fish white muscle: 1 -sarcoplasmic (around 30% of muscle protein, low salt soluble, enriched in enzymes); 2 -myofibrillar (around 60% of muscle protein, high salt soluble, enriched in structural proteins); and 3 -Running title: Proteomics of fish white muscle stromal (less abundant, enriched in connective proteins). In the following section a detailed workflow for protein extraction from teleost fish white muscle that is compatible with SWATH proteomics analysis is outlined, using the European sea bass (Dicentrarchus labrax) as the example [7,8]. The protocol provides the main steps for efficient extraction of the three main protein fractions.…”