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Highlights • A SWATH-MS-based proteomics was used for origin tracing of A. japonicas products. • Comparative protein quantitation was performed using UHPLC-QTOF platform. • Geographical origin was determined by OPLS-DA modeling. • Seventeen proteins were proposed as potential biomarkers. Abstract The article reports on discrimination of dried sea cucumber Apostichopus japonicus (A. japonicus) products from different geographical regions in China (Xiapu, Jiaonan, Weihai, Yantai, Dalian). For this purpose, sequential window acquisition of all theoretical fragment ion mass spectra (SWATH-MS)-based proteomic analysis combined with chemometrics was evaluated. Proteome variations of A. japonicus samples determined by SWATH-MS using ultra-high performance liquid chromatography coupled to quadrupole time of flight mass spectrometer were mined by chemometric tools to clarify the correlation between protein quantitation data and geographical origin. A differentiating OPLS-DA model was constructed with 55 SWATH-MS quantified proteins. A. japonicus samples from five locations were clearly classified by the developed OPLS-DA model and 100% prediction accuracy was achieved in validation testing as well as real-life sample analysis. Seventeen proteins were identified as discriminatory biomarkers allowing geographical provenance. The proposed method might be applied in origin authentication of commercially dried A. japonicus products. [ABSTRACT FROM AUTHOR]

Yeast extract is increasingly becoming an attractive source for unraveling novel umami peptides that are healthier and more nutritious than traditional seasonings. In the present study, a strategy for screening novel umami peptides was established using mass spectrometry-based peptidomics combined with molecular interaction modeling, emphasizing on smaller peptides than previously reported. Four representative novel umami peptides of FE, YDQ, FQEY, and SPFSQ from yeast extract (Saccharomyces cerevisiae) were identified and validated by sensory evaluation, with thresholds determined as 0.234 ± 0.045, 0.576 ± 0.175, 0.327 ± 0.057 and 0.456 ± 0.070 mmol/L, respectively. Hydrogen and ionic bonds were the main characteristic interactions between the umami peptides and the well-recognized receptor T1R1/T1R3, in which Asp 110, Thr 112, Arg 114, Arg 240, Lys 342, and Glu 264 were the key sites in ligand-receptor recognition. Our study provides accurate sequences of umami peptides and molecular interaction mechanism for the umami effect. [Display omitted] • Umami peptides were identified by UHPLC-MS/MS and de novo sequencing. • Four representative umami peptides from yeast extract were synthesized to verify the umami characteristic. • Asp 110, Thr 112, Arg 114, Arg 240, Lys 342, and Glu 264 were the key sites in ligand-receptor recognition. [ABSTRACT FROM AUTHOR]

Food fraud is common in the tuna industry because of the economic benefits involved. Ensuring the authenticity of tuna species is crucial for protecting both consumers and tuna stocks. In this study, GC-Q-TOF and UPLC-Q/Orbitrap mass spectrometry-based metabolomics were used to investigate the metabolite profiles of three commercial tuna species (skipjack tuna, bigeye tuna and yellowfin tuna). A total of 22 and 77 metabolites were identified with high confidence using GC-Q-TOF and UPLC-Q/Orbitrap mass spectrometry, respectively. Further screening via chemometrics revealed that 38 metabolites could potentially serve as potential biomarkers. Hierarchical cluster analysis showed that the screened metabolite biomarkers successfully distinguished the three tested tuna species. Furthermore, a total of 27 metabolic pathways were identified through enrichment analysis based on the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways. [ABSTRACT FROM AUTHOR]

• The effects of depuration salinity and duration on preservation were evaluated. • The mortality increased with 72 h depuration and 20% salinity fluctuation. • The SWATH-MS-based proteomic was developed to analysis protein changes. • 381 different expression proteins (DEPs) in total uncovered by proteomics analysis. • Most DEPs were relevant to amino acid metabolism. Depuration and anhydrous living-preservation are two important and consecutive steps during the circulation of Pacific oyster (Crassostrea gigas), and two main factors in depuration, salinity and duration, are pivotal to posterior anhydrous living-preservation of C. gigas. In this work, the comprehensive effects of depuration salinity (26–38 g/L) and duration (0–72 h) on anhydrous living-preservation at 4 °C for 7 days were investigated in regard of mortality, biochemical indexes (fatty acids profile analysis, glycogen) and proteome changes as well. The results showed that the mortality of C. gigas increased obviously with 72 h depuration and especially with 20 % salinity fluctuation, concomitantly accompanying metabolism disorder. Furthermore, alterations in salinity and duration resulted in 381 different expression proteins (DEPs), which were gotten more involved in the pathways related to amino acid metabolism. Taken together, it was suggested that duration < 48 h and salinity fluctuations lower than 10 % were the preferred conditions for anhydrous living-preservation. [ABSTRACT FROM AUTHOR]

• Proteome changes of A. japonicus after heat treatments were measured by SWATH-MS. • 24 and 13 proteins were indicators for heat treatment and three heat procedures. • Majority of the differentiating proteins were function relevant by GO annotation. The effects of heat treatment on the proteome of Apostichopus japonicus have been evaluated using label-free quantitative proteomics by ultrahigh performance liquid chromatography-quadrupole/time of flight (UHPLC-Q/TOF) mass spectrometry with sequential window acquisition of all the theoretical fragment ion (SWATH) acquisition mode. Chemometric tools are integrated to reveal proteomic changes by mining the protein quantitation data from fresh and differently heat-treated samples. SWATH allows the quantitation of 548 proteins, of which 24 proteins are significantly sensitive to heat treatment and 13 proteins vary significantly responding to different heat procedures (boiling, steaming, and microwave heating), and 5 of them are sharing proteins. Gene ontology (GO) annotation of the differentiating proteins highlights most of them are relevant to molecular functions. The results can be favorable to evaluate the effects of heat treatment on the nutrition and function of processed sea cucumbers and facilitate the selection of an optimal thermal treatment. [ABSTRACT FROM AUTHOR]

• Proteomic analysis revealed differentiating proteins (DPs) in C. gigas. • Levels of DPs associated with glycolysis increased with salinity stress. • Levels of DPs associated with ECM-receptor interaction pathway increased. • Depuration in 38 g/L salinity was detrimental to oyster quality. • Depuration salinity fluctuation should be controlled within ± 10% of production area. Salinity stress during depuration of Pacific oysters (Crassostrea gigas) leads to degradation in quality; therefore, an understanding of the molecular mechanisms regulating dynamic changes during depuration is needed. Here, C. gigas was depurated for 72 h at salinities ranging from 26 to 38 g/L, a ± 10–20% fluctuation from that in the production area, and the gill proteomes were analyzed by sequential window acquisition of all theoretical fragment ion mass spectra (SWATH-MS). Of the 1218 proteins analyzed, 241 were differentiating proteins (DPs). Salinity stress led to increased levels of DPs associated with glycolysis and the extracellular matrix–receptor interaction pathway, and decreased levels of DPs associated with the citric acid cycle, lipid metabolism, genetic information processing, and cell transformation, especially in oysters exposed to 38 g/L salinity (+20%). Controlling salinity fluctuation within ± 10% of the production area during depuration was conducive to maintaining quality in C. gigas. [ABSTRACT FROM AUTHOR]

• An HILIC-HRMS method was established to analyze sea cucumber gangliosides (SC-GLSs). • Neu5Gc, sulfated and fucosylated Neu5Gc were prevalently found in SC-GLSs. • Phosphoinositidyled GLSs were identified in SC-GLSs for the first time. • GD 4 and GD 4 (1S) were the dominant gangliosides in sea cucumbers. • SC-GLSs could structure-selectively promote the differentiation of PC12 cells. An HILIC-ESI-MS/MS method was established to analyze ganglioside (GLS) in sea cucumbers. In total, 17 GLS subclasses were detected in six sea cucumber species. The basic sea cucumber GLSs (SC-GLSs) were elucidated as NeuGc2-6Glc1-1Cer (SC-GM 4). The polymerization degree of the sialic acid (Sia) of SC-GLSs can be up to 4, and the linkage among Sias was mostly determined to be 2–8 or 2–11. Neu5Gc, sulfated and fucosylated NeuGc prevalently existed in SC-GLSs. Moreover, a new SC-GLSs structure with phosphoinositidyled Sia was first observed in Bohadschia marmorata. For the first time, we demonstrated that the content of SC-GD 4 , which is the dominant GLS in sea cucumbers, was 27–67%. Minor GLSs characterized as SC-GT 2 (Neu5GcMe) and SC-GQ 2 (Neu5GcMe) were also discovered. Additionally, SC-GD 4 and SC-GD 4 (1S) could significantly promote the differentiation of PC12 cells with structure-selectivity (p < 0.05). Our results provide insights into SC-GLSs to elucidate their Sia substituent and core saccharide chain linkage. [ABSTRACT FROM AUTHOR]