scholarly journals Analysis of Proteins Associated with Quality Deterioration of Grouper Fillets Based on TMT Quantitative Proteomics during Refrigerated Storage

Molecules ◽  
2019 ◽  
Vol 24 (14) ◽  
pp. 2641 ◽  
Author(s):  
Zhang ◽  
Xie
Keyword(s):  
Quantitative Proteomics ◽  
Interaction Network ◽  
Calcium Handling ◽  
Structural Proteins ◽  
Group Comparison ◽  
Refrigerated Storage ◽  
Loss Color ◽  
Go Enrichment ◽  
Tandem Mass Tag ◽  
Proteome Changes

A TMT (Tandem Mass Tag)-based strategy was applied to elucidate proteins that change in proteomes of grouper fillets during refrigerated storage. In addition, quality analyses on pH, centrifugal loss, color (L *, a *, b *) and texture (hardness, chewiness, and gumminess) for grouper fillets were performed. A total of 64 differentially significant expressed proteins (DSEPs) were found in the results in the Day 0 vs. Day 6 group comparison and the Day 0 vs. Day 12 group comparison. It is worth mentioning that more proteome changes were found in the Day 0 vs. Day 12 comparisons. Bioinformatics was utilized to analyze the DSEP. UniProt Knowledgebase (UniProtKB), Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein interaction network analysis were adopted. All DSEPs were classified into seven areas by function: binding proteins, calcium handling, enzymes, heat shock protein, protein turnover, structural proteins and miscellaneous. The numbers of proteins that correlated closely with pH, centrifugal loss, color (L *, a *, b *) and texture (hardness, chewiness, and gumminess) were 4, 3, 6 and 8, respectively.

scholarly journals Differentially Expressed Protein Analysis of Placenta from Women with Gestational Diabetes Mellitus using Tandem Mass Tag Quantitative Proteomics

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Sun X ◽  
◽  
Qu T ◽  
Yang X ◽  
He X ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Gestational Diabetes ◽  
Gestational Diabetes Mellitus ◽  
Protein Interaction Network ◽  
Quantitative Proteomics ◽  
Interaction Network ◽  
Differentially Expressed ◽  
Tandem Mass ◽  
Differentially Expressed Proteins ◽  
Tandem Mass Tag

Gestational Diabetes Mellitus (GDM) is one of the diseases occurring in pregnancy. Although normal postpartum glycometabolism can be restored in most patients with GDM, they have a significantly increased risk of developing complications in the future. In recent years, many studies on the screening of differentially expressed proteins have been performed in patients with GDM by means of proteomics, but the pathogenesis of GDM in the placenta was still unclear. Thus, using the Tandem Mass Tag (TMT) quantitative technology, we aimed to identify candidate biomarkers that could predict GDM occurrence early and provide targets for future therapy. Placenta samples were obtained from pregnant women immediately after delivery. Quantitative proteomics was performed using TMT isobaric tags and liquid chromatography-tandem mass spectrometry. Bioinformatic analysis was performed to elucidate the biological processes that these differentially expressed proteins were involved in. Thirtyfive differentially expressed proteins were identified between patients with GDM and normal pregnant women. Therein, 7 and 28 proteins were upregulated and downregulated, respectively. Differentially expressed proteins were mainly enriched in African trypanosomiasis pathway, hematopoietic cell lineage, gap junction, glucagon signaling pathway, and retinol metabolism. Insulin resistance induced by the excessively activated glucagon signaling pathway in the placenta may be one of the reasons for GDM onset. Among the 35 differentially expressed proteins, excluding 12 unknown proteins or antibodies, 17 of the remaining 23 proteins converged to the same protein-protein interaction network, indicating that a highly linked protein interaction network in the placenta of patients with GDM affected the occurrence of disease.

Identification of novel autoantibodies in ascites of relapsed paclitaxel-resistant gastric cancer with peritoneal metastasis using immunome protein microarrays and proteomics

2021 ◽  
pp. 1-10
Author(s):  
Zhongyin Yang ◽  
Chao Yan ◽  
Wentao Liu ◽  
Wei Xu ◽  
Chen Li ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Effective Treatment ◽  
Peritoneal Metastasis ◽  
Quantitative Proteomics ◽  
Poor Prognosis ◽  
Protein Microarrays ◽  
Tandem Mass ◽  
Tandem Mass Tag ◽  
Resistant Group ◽  
Potential Biomarkers

BACKGROUND: Gastric cancer (GC) patients with peritoneal metastasis usually have extremely poor prognosis. Intraperitoneal infusion of paclitaxel (PTX) provides an effective treatment, but relapse and PTX-resistance are unavoidable disadvantages, and it is difficult to monitor the occurrence of PTX-resistance. OBJECTIVE: The aim of this study was to explore novel autoantibodies in the ascites of individuals with relapsed PTX-resistant GC with peritoneal metastasis. METHODS: Ascites samples were collected before PTX infusion and after the relapse in 3 GC patients. To determine the expression of significantly changed proteins, we performed autoantibody profiling with immunome protein microarrays and tandem mass tag (TMT) quantitative proteomics, and then, the overlapping proteins were selected. RESULTS: Thirty-eight autoantibodies that were differentially expressed between the ascites in the untreated group and relapsed PTX-resistant group were identified. For confirmation of the results, TMT quantitative proteomics was performed, and 842 dysregulated proteins were identified. Four proteins, TPM3, EFHD2, KRT19 and vimentin, overlapped between these two assays. CONCLUSIONS: Our results first revealed that TPM3, EFHD2, KRT19 and vimentin were novel autoantibodies in the ascites of relapsed PTX-resistant GC patients. These autoantibodies may be used as potential biomarkers to monitor the occurrence of PTX-resistance.

scholarly journals Oxonium Ion Guided Analysis of Quantitative Proteomics Data Reveals Site-Specific O-Glycosylation of Anterior Gradient Protein 2 (AGR2)

2021 ◽  
Vol 22 (10) ◽  
pp. 5369
Author(s):  
Martina Pirro ◽  
Yassene Mohammed ◽  
Arnoud H. de Ru ◽  
George M. C. Janssen ◽  
Rayman T. N. Tjokrodirijo ◽  
...  
Keyword(s):  
Cell Lines ◽  
Quantitative Proteomics ◽  
Glycosylation Site ◽  
Total Cell ◽  
Tandem Mass ◽  
Proteomics Data ◽  
Site Specific ◽  
Oxonium Ions ◽  
Tandem Mass Tag ◽  
Colorectal Cancer Cell Lines

Developments in mass spectrometry (MS)-based analyses of glycoproteins have been important to study changes in glycosylation related to disease. Recently, the characteristic pattern of oxonium ions in glycopeptide fragmentation spectra had been used to assign different sets of glycopeptides. In particular, this was helpful to discriminate between O-GalNAc and O-GlcNAc. Here, we thought to investigate how such information can be used to examine quantitative proteomics data. For this purpose, we used tandem mass tag (TMT)-labeled samples from total cell lysates and secreted proteins from three different colorectal cancer cell lines. Following automated glycopeptide assignment (Byonic) and evaluation of the presence and relative intensity of oxonium ions, we observed that, in particular, the ratio of the ions at m/z 144.066 and 138.055, respectively, could be used to discriminate between O-GlcNAcylated and O-GalNAcylated peptides, with concomitant relative quantification between the different cell lines. Among the O-GalNAcylated proteins, we also observed anterior gradient protein 2 (AGR2), a protein which glycosylation site and status was hitherto not well documented. Using a combination of multiple fragmentation methods, we then not only assigned the site of modification, but also showed different glycosylation between intracellular (ER-resident) and secreted AGR2. Overall, our study shows the potential of broad application of the use of the relative intensities of oxonium ions for the confident assignment of glycopeptides, even in complex proteomics datasets.

scholarly journals Quantitative Proteomics Analysis Reveals the Function of the Putative Ester Cyclase UvEC1 in the Pathogenicity of the Rice False Smut Fungus Ustilaginoidea virens

2021 ◽  
Vol 22 (8) ◽  
pp. 4069
Author(s):  
Xiaoyang Chen ◽  
Zhangxin Pei ◽  
Pingping Li ◽  
Xiabing Li ◽  
Yuhang Duan ◽  
...  
Keyword(s):  
Quantitative Proteomics ◽  
Fungal Pathogens ◽  
Protein Localization ◽  
Proteomics Data ◽  
Ustilaginoidea Virens ◽  
Rice False Smut ◽  
Oxidative Stresses ◽  
Tandem Mass Tag ◽  
Cyclase Domain ◽  
False Smut

Rice false smut is a fungal disease distributed worldwide and caused by Ustilaginoidea virens. In this study, we identified a putative ester cyclase (named as UvEC1) as being significantly upregulated during U. virens infection. UvEC1 contained a SnoaL-like polyketide cyclase domain, but the functions of ketone cyclases such as SnoaL in plant fungal pathogens remain unclear. Deletion of UvEC1 caused defects in vegetative growth and conidiation. UvEC1 was also required for response to hyperosmotic and oxidative stresses and for maintenance of cell wall integrity. Importantly, ΔUvEC1 mutants exhibited reduced virulence. We performed a tandem mass tag (TMT)-based quantitative proteomic analysis to identify differentially accumulating proteins (DAPs) between the ΔUvEC1-1 mutant and the wild-type isolate HWD-2. Proteomics data revealed that UvEC1 has a variety of effects on metabolism, protein localization, catalytic activity, binding, toxin biosynthesis and the spliceosome. Taken together, our findings suggest that UvEC1 is critical for the development and virulence of U. virens.

scholarly journals Tandem Mass Tag-Based Quantitative Proteomics and Virulence Phenotype of Hemolymph-Treated Bacillus thuringiensis kurstaki Cells Reveal New Insights on Bacterial Pathogenesis in Insects

2021 ◽  
Author(s):  
Yanyan Sun ◽  
Linlin Yang ◽  
Lianet Rodríguez-Cabrera ◽  
Yushan Ding ◽  
Chaoliang Leng ◽  
...  
Keyword(s):  
Bacillus Thuringiensis ◽  
Quantitative Proteomics ◽  
Bacterial Pathogenesis ◽  
Midgut Epithelium ◽  
Tandem Mass ◽  
Content Type ◽  
Virulence Phenotype ◽  
Bacillus Thuringiensis Kurstaki ◽  
Tandem Mass Tag ◽  
Mass Tag

After ingestion by a susceptible insect and damaging its midgut epithelium, the bacterium Bacillus thuringiensis (Bt) reaches the insect blood (hemolymph), where it propagates despite the host’s antimicrobial defenses and induces insect death by acute septicemia. Although the hemolymph stage of the Bt toxic pathway is determinant for the infested insects’ fate, the response of Bt to hemolymph and the latter’s role in bacterial pathogenesis has been poorly explored.

Tandem mass tag-based quantitative proteomics analyses reveal the response of Bacillus licheniformis to high growth temperatures

2017 ◽  
Vol 67 (7) ◽  
pp. 501-510 ◽  
Author(s):  
Zixing Dong ◽  
Zhixin Chen ◽  
Hongbin Wang ◽  
Kangming Tian ◽  
Peng Jin ◽  
...  
Keyword(s):  
Bacillus Licheniformis ◽  
Quantitative Proteomics ◽  
High Growth ◽  
Tandem Mass ◽  
Tandem Mass Tag ◽  
Mass Tag

scholarly journals Revealing the Therapeutic Targets and Mechanism of Baicalin for Anti-chronic Gastritis Through TMT Proteomic Approach

2021 ◽  
Author(s):  
Wanli Ji ◽  
Yan Huo ◽  
Yu Zhang ◽  
Xinhong Wang ◽  
Yifan Zhang
Keyword(s):  
Chronic Gastritis ◽  
Therapeutic Targets ◽  
Interaction Network ◽  
B Cell Lymphoma ◽  
Treated Group ◽  
Sprague Dawley ◽  
Protein Protein Interaction ◽  
Proteomic Approach ◽  
Proteome Changes ◽  
Factor Α

Abstract BackgroundBaicalin (BCL) is a natural compound with beneficial activities, including antioxidant, anti-inflammatory and immunomodulatory. To investigate the therapeutic action of baicalin treatment in ethanol-induced chronic gastritis. Here, we investigated the proteome changes in the gastric tissue to elucidate the therapeutic targets of baicalin in chronic gastritis by TMT-based quantitative proteomics.ResultsUsing TMT-based quantitative proteomics, a total of the 4,452 proteins were identified and quantified in the gastric antrum tissue of Sprague–Dawley rats. Of these, 107 differentially expressed proteins, including 44 up-regulated and 63 down-regulated proteins, were uncovered in the baicalin-treated group as compared with the untreated group with ethanol-induced gastritis. Furthermore, the expression of TPM2, GIMAP4, and Mpc1 was validated using Western Blot. Baicalin could decrease the production of interleukin (IL)-2, IL-8 and tumor necrosis factor-α (TNF-α), while increase the expression of epidermal growth factor (EGF) and B-cell lymphoma-2 (Bcl-2). Notably, protein-protein interaction network analysis revealed the widespread interactions mediated by baicalin.ConclusionsWe investigated the effects and potential mechanism of baicalin in chronic gastritis. Proteomic technology was used to explore baicalin-affected proteins and some signaling pathways. The results may provide important insights into the discovery of potential target proteins for the treatment of chronic gastritis.

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