Proteomic Analysis of Beef Tenderloin and Flank Assessed Using an Isobaric Tag for Relative and Absolute Quantitation (iTRAQ)

Herein, we performed a proteomic analysis of tenderloin and flank steaks from Simmental cattle using the isobaric tags for a relative and absolute quantification (iTRAQ) approach. We identified 17 amino acids in both steaks, and Gly, Cys, Ile, Lys, and Pro differed most in abundance between the steak types (p < 0.05). A comparison of the expression patterns in steaks revealed 128 differentially expressed proteins (DEPs), of which 44 were up-regulated and 84 were down-regulated. Furthermore, 27 DEPs (p < 0.05) were subjected to gene ontology (GO) analysis, and many were found to be related to oxidation-reduction, metabolism, hydrogen ion transmembrane transport, transport, the tricarboxylic acid (TCA) cycle, mitochondrial electron transport, and the conversion of nicotinamide adenine dinucleotide (NADH) to ubiquinone. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis also implicated these DEPs in various signalling pathways, including oxidative phosphorylation, cardiac muscle contraction, the TCA cycle, biosynthesis, and the metabolism. These findings provide a new insight into key proteins involved in the determination of amino acid composition in beef.

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Proteomic Analysis of Rapeseed Root Response to Waterlogging Stress

Plants ◽

10.3390/plants7030071 ◽

2018 ◽

Vol 7 (3) ◽

pp. 71 ◽

Cited By ~ 5

Author(s):

Jinsong Xu ◽

Xing Qiao ◽

Zhitao Tian ◽

Xuekun Zhang ◽

Xiling Zou ◽

...

Keyword(s):

Proteomic Analysis ◽

Molecular Mechanisms ◽

Yangtze River Basin ◽

Reduction Process ◽

Absolute Quantification ◽

Brassica Napus L ◽

Waterlogging Stress ◽

Oxidation Reduction ◽

Root Response ◽

Isobaric Tags

The overall health of a plant is constantly affected by the changing and hostile environment. Due to climate change and the farming pattern of rice (Oryza sativa) and rapeseed (Brassica napus L.), stress from waterlogging poses a serious threat to productivity assurance and the yield of rapeseed in China’s Yangtze River basin. In order to improve our understanding of the complex mechanisms behind waterlogging stress and identify waterlogging-responsive proteins, we firstly conducted iTRAQ (isobaric tags for relative and absolute quantification)-based quantitative proteomic analysis of rapeseed roots under waterlogging treatments, for both a tolerant cultivar ZS9 and sensitive cultivar GH01. A total of 7736 proteins were identified by iTRAQ, of which several hundred showed different expression levels, including 233, 365, and 326 after waterlogging stress for 4H, 8H, and 12H in ZS9, respectively, and 143, 175, and 374 after waterlogging stress for 4H, 8H, and 12H in GH01, respectively. For proteins repeatedly identified at different time points, gene ontology (GO) cluster analysis suggested that the responsive proteins of the two cultivars were both enriched in the biological process of DNA-dependent transcription and the oxidation–reduction process, and response to various stress and hormone stimulus, while different distribution frequencies in the two cultivars was investigated. Moreover, overlap proteins with similar or opposite tendencies of fold change between ZS9 and GH01 were observed and clustered based on the different expression ratios, suggesting the two genotype cultivars exhibited diversiform molecular mechanisms or regulation pathways in their waterlogging stress response. The following qRT-PCR (quantitative real-time polymerase chain reaction) results verified the candidate proteins at transcription levels, which were prepared for further research. In conclusion, proteins detected in this study might perform different functions in waterlogging responses and would provide information conducive to better understanding adaptive mechanisms under environmental stresses.

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Isobaric Tags for Relative and Absolute Quantitation–Based Proteomic Analysis of Patent and Constricted Ductus Arteriosus Tissues Confirms the Systemic Regulation of Ductus Arteriosus Closure

Journal of Cardiovascular Pharmacology ◽

10.1097/fjc.0000000000000266 ◽

2015 ◽

Vol 66 (2) ◽

pp. 204-213 ◽

Cited By ~ 3

Author(s):

Haifa Hong ◽

Lincai Ye ◽

Huiwen Chen ◽

Yu Xia ◽

Yue Liu ◽

...

Keyword(s):

Proteomic Analysis ◽

Ductus Arteriosus ◽

Absolute Quantitation ◽

Isobaric Tags

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Prospect and Competence of Quantitative Methods via Real-time PCR in a Comparative Manner: An Experimental Review of Current Methods

The Open Bioinformatics Journal ◽

10.2174/1875036201811010001 ◽

2018 ◽

Vol 11 (1) ◽

pp. 1-11

Author(s):

Hossein Mahboudi ◽

Negin Mohammadizadeh Heidari ◽

Zahra Irani Rashidabadi ◽

Ali Houshmand Anbarestani ◽

Soroush Karimi ◽

...

Keyword(s):

Internal Control ◽

Copy Number ◽

Quantitative Methods ◽

Absolute Quantification ◽

Relative Quantification ◽

Absolute Quantitation ◽

Standard Curve ◽

Qpcr Quantification ◽

Comparative Manner

Background: There are numerous approaches dealing with relative and absolute quantitation. The methods differ in their efficiency assumption and applicability. Objective: Current methodologies and rations used in qPCR quantification were compared in an experimental study of transgenic copy number determination of a monoclonal antibody Daclizumab. Methods: With an inter and intra-methodical view, variations in relative and absolute quantification strategies were discretely extracted and compared to one another. Results: In relative quantification, six methods were studied and the ratios were computed relative to Glucagon as internal control. For Absolute quantification, the calculations were based on standard curve. Relative quantification considers the relative changes in expression levels while Absolute quantification relates the PCR signal to input copy number with a calibration curve. Conclusion: The observed unevenness of the ratios in Relative approach pointed mainly to the efficiency changes and its calculation formula. Whereas results in Absolute approach strategies showed homogeneity which indicates the consistency of the calculation method.

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Cellular proteomic analysis of porcine circovirus type 2 and classical swine fever virus coinfection in porcine kidney-15 cells using isobaric tags for relative and absolute quantitation-coupled LC-MS/MS

Electrophoresis ◽

10.1002/elps.201600541 ◽

2017 ◽

Vol 38 (9-10) ◽

pp. 1276-1291 ◽

Cited By ~ 6

Author(s):

Niu Zhou ◽

Chunmei Fan ◽

Song Liu ◽

Jianwei Zhou ◽

Yulan Jin ◽

...

Keyword(s):

Classical Swine Fever Virus ◽

Proteomic Analysis ◽

Classical Swine Fever ◽

Porcine Circovirus Type ◽

Fever Virus ◽

Porcine Circovirus ◽

Porcine Kidney ◽

Absolute Quantitation ◽

Isobaric Tags

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Comparative Proteomic Analysis of Dipsacus asperoides Roots from Different Habitats in China

Molecules ◽

10.3390/molecules25163605 ◽

2020 ◽

Vol 25 (16) ◽

pp. 3605

Author(s):

Haijun Jin ◽

Hua Yu ◽

Haixia Wang ◽

Jia Zhang

Keyword(s):

Proteomic Analysis ◽

Absolute Quantification ◽

Pcr Analysis ◽

Allene Oxide ◽

Allene Oxide Cyclase ◽

Protein Levels ◽

Depth Analysis ◽

Differential Proteins ◽

Isobaric Tags

Dipsacus asperoides is a kind of Chinese herbal medicine with beneficial health properties. To date, the quality of D. asperoides from different habitats has shown significant differences. However, the molecular differences in D. asperoides from different habitats are still unknown. The aim of this study was to investigate the differences in protein levels of D. asperoides from different habitats. Isobaric tags for relative and absolute quantification (iTRAQ) and 2DLC/MS/MS were used to detect statistically significant changes in D. asperoides from different habitats. Through proteomic analysis, a total of 2149 proteins were identified, of which 42 important differentially expressed proteins were screened. Through in-depth analysis of differential proteins, the protein metabolism energy and carbohydrate metabolism of D. asperoides from Hubei Province were strong, but their antioxidant capacity was weak. We found that three proteins, UTP-glucose-1-phosphate uridylyltransferase, allene oxide cyclase, and isopentyl diphosphate isomerase 2, may be the key proteins involved in dipsacus saponin VI synthesis. Eight proteins were found in D. asperoides in response to environmental stress from different habitats. Quantitative real-time PCR analysis confirmed the accuracy and authenticity of the proteomic analysis. The results of this study may provide the basic information for exploring the cause of differences in secondary metabolites in different habitats of D. asperoides and the protein mechanism governing differences in quality.

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