Search

Silkworm (Bombyx mori) pupae lipid profiles were analyzed using high-resolution mass spectrometry-based lipidomics. A total of 241 lipid molecular species were annotated with high confidence in male and female silkworm pupae. Triacylglycerol (TG), phosphoethanolamine (PE) and phosphocholine (PC) were the main lipid subclasses of silkworm pupae, accounting for 63, 41 and 38 lipid molecular species, respectively. No unique lipid molecular species were identified, but there were differences in the abundance of lipid molecular species between male and female silkworm pupae. Therefore, the differences in the lipid abundance of male and female silkworm pupae were analyzed by chemometrics. As a result, 8 lipid molecular species were screened for differential lipids. Hierarchical clustering analysis (HCA) showed that male and female silkworm pupae samples formed two distinct branches, indicating that these differential lipids could potentially be used as biomarkers to distinguish between male and female silkworm pupae., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

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., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

One of the challenges for cancer vaccine and adoptive T-cell-based immunotherapy is to identify the major histocompatibility complex (MHC)-associated non-self neoantigens recognized by T cells. T cell epitope in silico prediction algorithms have been widely used for neoantigen prediction; nonetheless, this platform lacks the experimental evidence of directly identification of the presented epitopes on cell surface. Currently, mass spectrometry (MS)-based proteomics is an advanced analytical technology for large-scale peptide sequencing, which has become a powerful tool for directly profiling the immunopeptidome presented by MHC molecules. Integrating with next-generation sequencing, proteogenomic analysis provides the "gold standard" for neoantigen identification at protein level. This method discovers the tumor-specific neoantigens derived from somatic mutations, proteasome splicing, noncoding RNA, and post-translational modified antigens. Herein, we review basis of antigen processing and presentation, tumor antigen classification, existing approaches for neoantigen discovery, quantitative proteomics, epitope prediction programs, and advantages and drawbacks of proteomics workflow for MHC immunopeptidome profiling. Furthermore, we summarize 40 recently published reports addressing the fundamental theory, breakthrough and most advanced updates for the mass spectrometry-based neoantigen discovery for cancer immunotherapy., (Copyright © 2019 The Authors. Published by Elsevier Masson SAS.. All rights reserved.)

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., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Incorrect labeling and adulteration of shrimp occurs due to interspecies similarities and carapace removal during processing. This study attempted to identify three related commercial shrimp species of the order Decapoda: Marsupenaeus japonicus, Fenneropenaeus chinensis, and Litopenaeus vannamei. All measurable trypsin-digested peptides in the individual shrimp were detected using ultrahigh-performance liquid chromatography quadrupole time-of-flight (UPLC-Q-TOF) mass spectrometry with sequential window acquisition of all theoretical fragment ion spectra (SWATH) data-independent acquisition. Further analysis of peptide biomarkers was carried out with an orthogonal partial least-squares discriminant analysis (OPLS-DA) model. BLAST was used for species-specific analysis. Subsequently, multiple reaction monitoring (MRM) methods were developed for sensitivity and selectivity screening of the selected peptides, and 27 were identified as biomarkers allowing rapid and accurate discrimination of shrimp species without high-resolution mass spectrometry or statistical model building. These strategies could be applied in authentication of other products containing highly homologous proteomes.

A novel method was established for the determination of six plant growth regulators (PGRs), 2,4-dichlorophenoxy acetic (2,4-D), 4-chlorophenoxy-acetic acid (CAP), 4-(3-indolyl)-butyric acid (BAA), forchlorfenuron (CPPU), abscisic acid (ABA) and trans-zeatin (ZT) in strawberry using liquid chromatography-quadrupole-time of flight mass spectrometry (LC-Q TOF MS). The Quick, Easy, Cheap, Effective, Rugged and Safe method (QuEChERS) has been validated for the extraction. In this QuEChERS method, the sample was extracted by acetonitrile and cleaned up with C18 adsorbent. The extract was measured directly by LC-Q TOF MS with electrospray ionization in negative mode. The compounds were separated on an Eclipse XDB-C8 column (150 mm x 4.6 mm, 5 microm) with acetonitrile-5 mmol/L ammonium acetate-0. 1% formic acid as mobile phase under gradient elution. The confirmatory analysis was carried out by determining the accurate masses of all compounds and fragment ions upon Target MS/MS. The limits of detection (LODs) were between 1 microg/kg and 5 microg/kg. The linear range was 0.005-1.0 mg/L for each analyte. The recoveries ranged from 87% to 107% with the relative standard deviations (RSDs) less than 10% (n = 6). The method was proved to be simple and accurate.

Objective: This study was undertaken to elucidate the pathogenesis and heterogeneity of Behçet's disease (BD) involving different organs using in‐depth proteomics to identify the biomarkers for clinical assessment and treatment of patients with BD. Methods: We measured the expression levels of proteins in plasma samples from 98 patients with BD and from 31 healthy controls using our in‐depth proteomics platform with a data‐independent acquisition mass spectrometer and antibody microarray. We performed bioinformatics analyses of the biologic processes and signaling pathways that were changed in the BD group and constructed a proteomics landscape of organ‐resolved BD pathogenesis. We then validated the biomarkers of disease severity and the vascular subset in an independent cohort of 108 BD patients and 29 healthy controls using an enzyme‐linked immunosorbent assay. Results: The BD group had 220 differentially expressed proteins, which discriminated between BD patients (88.6%) and healthy controls (95.5%). The bioinformatics analyses revealed different biologic processes associated with BD pathogeneses, including complement activation, wound healing, angiogenesis, and leukocyte‐mediated immunity. Furthermore, the constructed proteomics landscape of organ‐resolved BD identified proteomics features of BD associated with different organs and protein targets that could be used for the development of therapeutic treatment. Hyaluronic binding protein 2, tenascin, and serpin A3 were validated as potential biomarkers for the clinical assessment of vascular BD and treatment targets. Conclusion: Our results provide valuable insight into the pathogenesis of organ‐resolved BD in terms of proteomics characteristics and potential biomarkers for clinical assessment and potential therapies for vascular BD. [ABSTRACT FROM AUTHOR]

Psoraleae Fructus (PF) is a botanical medicine widely used in Asian countries, of which salt products have higher safety and efficacy. However, the biological mechanism of the detoxification of salt-processing Psoraleae Fructus (SPF) has not yet been revealed. In this study, UPLC-MS/MS technology was used to explore the metabolic differences between SPF and PF in normal rats and reveal the mechanism of salt processing. The histopathological results of rat liver and kidney showed that the degree of liver and kidney injure in the SPF group was less than that in the PF group. The results of metabolomics showed that the detoxification mechanism of PF by salt processing might be related to glycerophospholipid metabolism, phenylalanine, tyrosine, and tryptophan biosynthesis, arginine and proline metabolism, phenylalanine metabolism, and linoleic acid metabolism. PF-induced inflammation could be reduced by regulating the expression of metabolites to achieve the purpose of salt processing and detoxification. It included reducing the production of metabolites such as 1-acyl-sn-glycero-3-phosphocholine, sn-glycero-3-phosphocholine, tyrosine, arginine, linoleic acid, arachidonic acid, and phenylacetylglycine/hippuric acid ratio and upregulating the expression of metabolites such as creatine. [ABSTRACT FROM AUTHOR]

The focus of this paper was to investigate the potential of distinguishing sea cucumbers from different production methods (farmed vs wild-caught) and different seasons (autumn vs summer) at the proteomic level. Based on biological mass spectrometry with sequential window acquisition of all the theoretical fragment ion mass spectra (SWATH) acquisition mode, the proteomes of Apostichopus japonicus under farmed and wild production methods were profiled and relatively quantified. The SWATH data were mined by chemometric tools aiming to screen protein biomarkers for the traceability of sea cucumbers in terms of production methods as well as harvesting seasons, respectively. In the end, 4 production-method-sensitive proteins regardless of harvesting seasons and 12 season-sensitive proteins regardless of production methods were unveiled. The protein biomarkers were visually validated by hierarchical clustering heatmap analysis, and gene ontology annotation of biomarkers provided more insight for understanding the intrinsic linkage between the traceability and function of Apostichopus japonicus. [Display omitted] • The proteome of A. japonicus from different methods and seasons were investigated. • Four production-sensitive and 12 season-sensitive protein biomarkers were obtained. • The sensitive protein biomarkers were functionally annotated by GO analysis. • The intrinsic linkage between the protein and production origins was revealed. [ABSTRACT FROM AUTHOR]

Salinity plays an important role in the environmental adaptability of Pacific oysters (Crassostrea gigas), whereas the molecular regulation mechanism of the organism responding to acute and longer-term chronic salinity stress remains unknown. In the present study, the proteome of C. gigas under acute salinity stress (exposed to the given salinity directly for 3 days) and longer-term chronic salinity stress (exposed to gradually changing salinity at a rate of one unit per day until the given salinity was reached and the total duration of exposure was one month) was quantitatively compared using sequential window acquisition of all theoretical fragment ion mass spectra (SWATH-MS). SWATH-MS data of 880 proteins were subjected to chemometric differentiation analysis, and 55 proteins were selected as differentiators responding to acute and longer-term chronic salinity stress. Most of the differentiating proteins (DPs) were attributed to cellular components by Gene Ontology (GO) annotation analysis. Additionally, mRNA expression of the DPs measured by real-time polymerase chain reaction (RT–PCR) verified similarities and differences in the expression level between mRNA and protein, whereas some tendencies were meaningful for mechanistic understanding. The proteins glutathione S-transferase, histone H2B, and thymosin β were finally suggested as biomarkers of C. gigas exposed to salinity stress. • The protein of acute and longer-term chronic salinity stress treatment was analyzed. • The SWATH-MS-based proteomic method was developed to reveal proteomic changes. • 880 proteins were subjected to SWATH-MS quantitation. • Four proteins were proposed as potential markers for stress evaluating of C. gigas. [ABSTRACT FROM AUTHOR]

• Peptides marking meat of fur-producing animals were explored by shot-gun proteomics. • DQTLQEELAR was verified to discern non-edible meat with detection level as 1% (w/w). • An MRM method was developed for risk control of non-edible meat adulteration. Non-edible meat from fur-producing animals entering into meat consumption chain could pose a serious threat to public health. For the purpose of risk prevention and control of meat safety, in this study, marker peptides for discriminating non-edible meat of fur-producing animals (including fox, silver fox, blue fox, raccoon dog, ussuri raccoon dog, mink and American mink) from meat of food-providing animals (including pig, cattle, sheep and donkey) were explored by shot-gun proteomics and verified by target approach. Two mass spectrometry platforms combined with bioinformatic and chemometric tools were integratedly emloyed for method development. Meat samples were first subjected to in-solution protein digestion and the subsequently tryptic peptides were profiled and quantitated by ultra-high pressure liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-Q/TOF MS) with sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) mode. Candidate marker peptides screened by chemometric tools were further filtered for their biological specificity and detectability through bioinformatics analysis as well as multiple reaction monitoring (MRM) verification with UHPLC-triple quadrupole mass spectrometry (UHPLC-QQQ MS). As a result, 9 peptides, out of 104 candidates, were selected as markers for discriminating analysis, of which DQTLQEELAR was validated as primary indicator of non-edible meat from the concerned fur-producing animals. An MRM method based on the developed marker peptides for routine use was finally proposed for risk alarming of non-edible meat from fur-producing animals in food safety control. [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]

[Display omitted] • Peptides of 45 tuna samples and 15 processed real samples of 3 types were detected. • Venn analysis showed the peptides of three tuna species were quite different. • The screened peptide biomarkers were effective in discriminating three tuna species. The risk of tuna adulteration is high driven by economic benefits. The authenticity of tuna is required to protect both consumers and tuna stocks. Given this, the study is designed to identify species-specific peptides for distinguishing three commercial tropical tuna species. The peptides derived from trypsin digestion were separated and detected using ultrahigh-performance liquid chromatography-quadrupole-time of flight mass spectrometry (UPLC-Q-TOF/MS) in data-dependent acquisition (DDA) mode. Venn analysis showed that there were differences in peptide composition among the three tested tuna species. The biological specificity screening through the National Center for Biotechnology Information's Basic Local Alignment Search Tool (NCBI BLAST) revealed that 93 peptides could serve as potential species-specific peptides. Finally, the detection specificity of species-specific peptides of raw meats and processed products was carried out by multiple reaction monitoring (MRM) mode based on a Q-Trap mass spectrometer. The results showed that three, one and two peptides of Katsuwonus pelamis , Thunnus obesus and Thunnus albacores , respectively could serve as species-specific peptides. [ABSTRACT FROM AUTHOR]

• Transformation of aromatic layer during heating was influenced by coal rank. • The increase of naphthalene is accompanied by the generation of CO 2 and H 2 O. • The formation of 4 × 4 aromatic layer is accompanied by the generation of CH 4. Three vitrinite samples of different rank, denoted as V-YJL, V-AW, and V-J15, were investigated by in situ heating while in a High resolution transmission electron microscope (HRTEM) to study the aromatic structural transformations from 200 to 800 °C. Thermogravimetry coupled with Fourier transform infrared spectroscopy and mass spectrometry (TG-FTIR-MS) was employed to measure gaseous release from 30 to 900 °C. The relationships between aromatic structural transformations and gaseous release were also discussed in this work. The results showed that the rank of coal influenced the changes of aromatic layers. The change of naphthalene of low-rank coal (V-YJL, R = 0.61%) had four stages. For higher rank coals with R = 1.09% (V-AW) and R = 2.22% (V-J15), the changes of naphthalene had three and two stages, respectively. The increase in naphthalene content occurred at the same temperature with the release of CO 2 and H 2 O, suggesting the increase of naphthalene probably caused by the decomposing of oxygen-containing functional groups. The noticeable change in 4 × 4 aromatic layers is from 650 to 750 °C, accompanying CH 4 release, suggesting the increase of 4 × 4 aromatic layers may result from the break of bonds like aryl-methyl bonds or aryl-alkyl bonds. [ABSTRACT FROM AUTHOR]

Meconopsis quintuplinervia Regel (MQR) belongs to the opium poppy tree plant species, and it has heat purging, detoxification, diuretic, anti-inflammatory, and analgesic effects. MQR has liver-protective properties and can alleviate liver heat. Therefore, this study aimed to observe the effect of MQR extract on acute alcoholic liver injury in mice and explore the mechanism of action of ethyl acetate extract of MQR (MQR-E) on alcohol-induced liver injury in combination with the network pharmacology. To induce acute alcoholic liver injury, 52% of edible wine was administered at 12 mL/kg for 14 days. The pharmacodynamic results were used to screen the active site. MQR-E composition was analyzed based on UPLC-Q-TOF-MS, and relevant MQR-E and alcoholic liver disease (ALD) targets were screened using an online database. Then, Venn analysis of drug and disease-related targets was performed to obtain cross-targets. We investigated the protein-protein interaction network (PPI) of overlapping targets, the core targets were screened using the STRING database, and the DAVID database was chosen for GO and KEGG enrichment analysis of the central targets. Each of the four MQR extracts ameliorated alcoholic liver injury to varying degrees; the best results were achieved with MQR-E. MQR-E reduces liver index, serum transaminases, and fat accumulation, and attenuates ethanol-induced histopathological changes. The activities of hepatic superoxide dismutase (SOD) and glutathione peroxidase (GSH-PX) were increased, the content of malondialdehyde (MDA) was significantly reduced compared to the EtOH group, and MQR-E effectively mitigated the oxidative stress induced by ethanol in the liver. Thirty-six compounds were identified, and flavonoids were the most abundant. PPI network topology analysis was employed to assess 32 core targets: IL-6, TNF, STAT3, PPARA, and other inflammation and lipid metabolism related genes. Pathway analysis of GO and KEGG enrichment showed that the regulation of inflammatory factors and lipid metabolism were primarily involved. We concluded that MQR-E had protective effects against acute alcohol-induced liver injury in mice, and the mechanism could be linked to the inhibition of lipid peroxidation and oxidative stress. The mechanism by which MQR-E ameliorated ALD primarily involved regulating inflammatory factors and lipid metabolism based on the prediction of the network pharmacology. [Display omitted] • Modeling with edible wine is more relevant to human life. • Tibetan medicine MQR has been inspired in the direction of alcoholic liver treatment. • The effective part of MQR for alcoholic liver pharmacodynamic screening. • The mechanism may be related to oxidative stress. • Predicted to correlate with inflammatory response and lipid metabolism. [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]

The adulteration of tuna is found as attenuation of morphological characteristics during processing due to the exhaustion of tuna resource. The authenticity of tuna is now concentrated in the seafood supply chain. Protein, as the most important component of tuna muscle, plays a very important role in tuna. In this study, the protein relative quantitation of 3 commercial tuna species (skipjack tuna, bigeye tuna and yellowfin tuna) were revealed through the developed sequential window acquisition of all theoretical fragment ion mass spectra (SWATH-MS)-based proteomic analysis with 81 proteins being reliably quantified. Further protein biomarkers discovery was carried out by chemometrics, leading to 14 proteins screened as potential biomarkers. Hierarchical clustering analysis showed that the screened protein biomarkers have the ability to distinguish the 3 tuna species. Gene ontology (GO) annotation of the screened protein biomarkers most of them were relevant to molecular functions. • The protein profiles of 3 commercial tuna species were investigated. • The protein biomarkers were revealed by pairwise comparisons of the OPLS-DA models. • HCA showed that protein biomarkers were effective in species discrimination. • GO annotation revealed that most protein biomarkers were relevant to molecular functions. [ABSTRACT FROM AUTHOR]

[Display omitted] • The lipid profiles of 3 commercial tuna species were investigated. • The lipid biomarkers were reveal by pairwise comparisons of the OPLS-DA models. • Real samples verification showed that lipid biomarkers were effective in species discrimination. Mislabeling and adulteration of tuna are common due to the diminishing of morphological characteristics during processing. The tuna authenticity is now being focused in the seafood supply chain. In this study, the lipid profiles of 3 commercial tuna species (skipjack tuna, bigeye tuna and yellowfin tuna) were investigated via ultra-high performance liquid chromatography coupled with Q-Exactive Orbitrap mass spectrometry (UPLC-Q-Exactive Orbitrap MS). A total of 439 lipid species were identified and semi-quantitated by MS-DIAL. Further biomarkers discovery was carried out by chemometrics, leading to 27 lipids being identified as potential lipid biomarkers. Comparisons to reference standards revealed that lipid biomarkers were effective for discrimination of different tuna species. Interestingly, the proposed lipid biomarkers were all glycerophospholipids, implying that they might be the focus of future study. [ABSTRACT FROM AUTHOR]