Detection of differentially expressed Beta Amyloid fragments from Alzheimer's Patients by Mass Spectrometry

Introduction: The aim of this study was to investigate the modified proteins in methylene blue/light-treated frozen plasma (MB-FP) compared with fresh frozen plasma (FFP) in order to gain a better application of MB/light-treated plasma in clinic transfusion. Methods: MB-FP and FFP were collected from Changchun central blood station, and a trichloroacetic acid/acetone precipitation method was used to remove albumin for the enrichment of lower abundance proteins. The plasma protein in MB-FP and FFP were separated using two-dimensional gel electrophoresis (2-DE) and the differentially expressed protein spots were analyzed using mass spectrometry. Finally, the differentially expressed proteins were tested using Western blot and enzyme-linked immunosorbent assay (ELISA). Results: Approximately 14 differentially expressed protein spots were detected in the MB-FP, and FFP was chosen as the control. After 2-DE comparison analysis and mass spectrometry, 8 significantly differentially expressed protein spots were identified, corresponding to 6 different proteins, including complement C1r subcomponent (C1R), inter-alpha-trypsin inhibitor heavy chain H4 (ITI-H4), keratin, type II cytoskeletal 1 (KRT1), hemopexin (HPX), fibrinogen gamma chain (FGG), and transthyretin (TTR). Western blot showed no significant difference in the expression level of KRT1 between MB-FP and FFP (p > 0.05). Both Western blot and ELISA indicated that the level of HPX was significantly higher in FFP than in MB-FP (p < 0.05). Conclusion: This comparative proteomics study revealed that some significantly modified proteins occur in MB-FP, such as C1R, ITI-H4, KRT1, HPX, FGG, and TTR. Our findings provide more theoretical data for using MB-FP in transfusion medicine. However, the relevance of the data for the transfusion of methylene blue/light-treated plasma remains unclear. The exact modification of these proteins and the effects of these modified proteins on their functions and their effects in clinical plasma infusion need to be further studied.

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Identification of differentially expressed proteins in retinoblastoma tumors using mass spectrometry-based comparative proteomic approach

Journal of Proteomics ◽

10.1016/j.jprot.2017.02.006 ◽

2017 ◽

Vol 159 ◽

pp. 77-91 ◽

Cited By ~ 7

Author(s):

Jasmine Naru ◽

Ritu Aggarwal ◽

Ashok Kumar Mohanty ◽

Usha Singh ◽

Deepak Bansal ◽

...

Keyword(s):

Mass Spectrometry ◽

Differentially Expressed ◽

Differentially Expressed Proteins ◽

Proteomic Approach

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The gene for the Alzheimer-associated beta-amyloid-binding protein (ERAB) is differentially expressed in the testicular Leydig cells of the azoospermic by w/wv mouse

European Journal of Biochemistry ◽

10.1046/j.1432-1327.1998.2580053.x ◽

1998 ◽

Vol 258 (1) ◽

pp. 53-60 ◽

Cited By ~ 16

Author(s):

Christoph Hansis ◽

Detlev Jahner ◽

Andrej-Nikolai Spiess ◽

Kay Boettcher ◽

Richard Ivell

Keyword(s):

Leydig Cells ◽

Binding Protein ◽

Beta Amyloid ◽

Differentially Expressed

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Multi-Omics Characterization of Circular RNA-Encoded Novel Proteins Associated With Bladder Outlet Obstruction

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.772534 ◽

2022 ◽

Vol 9 ◽

Author(s):

Baoyi Zhu ◽

Zhanfang Kang ◽

Sihua Zhu ◽

Yuying Zhang ◽

Xiangmao Lai ◽

...

Keyword(s):

Mass Spectrometry ◽

Quantitative Proteomics ◽

Bladder Outlet Obstruction ◽

Molecular Mechanisms ◽

Outlet Obstruction ◽

Differentially Expressed ◽

Circular Rnas ◽

Protein Profiles ◽

Rt Pcr ◽

Novel Proteins

Bladder outlet obstruction (BOO) is a common urologic disease associated with poorly understood molecular mechanisms. This study aimed to investigate the possible involvements of circRNAs (circular RNAs) and circRNA-encoded proteins in BOO development. The rat BOO model was established by the partial bladder outlet obstruction surgery. Differential expression of circRNA and protein profiles were characterized by deep RNA sequencing and iTRAQ quantitative proteomics respectively. Novel proteins encoded by circRNAs were predicted through ORF (open reading frame) selection using the GETORF software and verified by the mass spectrometry in proteomics, combined with the validation of their expressional alterations by quantitative RT-PCR. Totally 3,051 circRNAs were differentially expressed in bladder tissues of rat BOO model with widespread genomic distributions, including 1,414 up-regulated, and 1,637 down-regulated circRNAs. Our following quantitative proteomics revealed significant changes of 85 proteins in rat BOO model, which were enriched in multiple biological processes and signaling pathways such as the PPAR and Wnt pathways. Among them, 21 differentially expressed proteins were predicted to be encoded by circRNAs and showed consistent circRNA and protein levels in rat BOO model. The expression levels of five protein-encoding circRNAs were further validated by quantitative RT-PCR and mass spectrometry. The circRNA and protein profiles were substantially altered in rat BOO model, with great expressional changes of circRNA-encoded novel proteins.

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Metabolome and Transcriptome Integration Reveals Insights Into Flavor Formation of ‘Crimson’ Watermelon Flesh During Fruit Development

Frontiers in Plant Science ◽

10.3389/fpls.2021.629361 ◽

2021 ◽

Vol 12 ◽

Author(s):

Chengsheng Gong ◽

Weinan Diao ◽

Hongju Zhu ◽

Muhammad Jawad Umer ◽

Shengjie Zhao ◽

...

Keyword(s):

Mass Spectrometry ◽

Fruit Development ◽

Developmental Stages ◽

Solid Phase ◽

Differentially Expressed ◽

Ultrahigh Performance Liquid Chromatography ◽

Fruit Flavor ◽

Metabolome Data ◽

Main Factor ◽

Comprehensive Study

Metabolites have been reported as the main factor that influences the fruit flavor of watermelon. But the comprehensive study on the dynamics of metabolites during the development of watermelon fruit is not up-to-date. In this study, metabolome and transcriptome datasets of ‘Crimson’ watermelon fruit at four key developmental stages were generated. A total of 517 metabolites were detected by ultrahigh-performance liquid chromatography–electrospray ionization–tandem mass spectrometry and gas chromatography–solid-phase microextraction–mass spectrometry. Meanwhile, by K-means clustering analysis, the total differentially expressed genes were clustered in six classes. Integrating transcriptome and metabolome data revealed similar expression trends of sugars and genes involved in the glycolytic pathway, providing molecular insights into the formation of taste during fruit development. Furthermore, through coexpression analysis, we identified five differentially expressed ADH (alcohol dehydrogenase) genes (Cla97C01G013600, Cla97C05G089700, Cla97C01G001290, Cla97C05G095170, and Cla97C06G118330), which were found to be closely related to C9 alcohols/aldehydes, providing information for the formation of fruit aroma. Our findings establish a metabolic profile during watermelon fruit development and provide insights into flavor formation.

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Proteomics Analysis Reveals the Implications of Cytoskeleton and Mitochondria in the Response of the Rat Brain to Starvation

Nutrients ◽

10.3390/nu11020219 ◽

2019 ◽

Vol 11 (2) ◽

pp. 219 ◽

Cited By ~ 1

Author(s):

Beatriz Cuevas-Fernández ◽

Carlos Fuentes-Almagro ◽

Juan Peragón

Keyword(s):

Mass Spectrometry ◽

Rat Brain ◽

Food Deprivation ◽

Metabolic Response ◽

Differentially Expressed ◽

Nervous Impulse ◽

Altered Expression ◽

Peptide Mass ◽

The Brain

Long-term starvation provokes a metabolic response in the brain to adapt to the lack of nutrient intake and to maintain the physiology of this organ. Here, we study the changes in the global proteomic profile of the rat brain after a seven-day period of food deprivation, to further our understanding of the biochemical and cellular mechanisms underlying the situations without food. We have used two-dimensional electrophoresis followed by mass spectrometry (2D-MS) in order to identify proteins differentially expressed during prolonged food deprivation. After the comparison of the protein profiles, 22 brain proteins were found with altered expression. Analysis by peptide mass fingerprinting and MS/MS (matrix-assisted laser desorption-ionization-time of flight mass spectrometer, MALDI-TOF/TOF) enabled the identification of 14 proteins differentially expressed that were divided into 3 categories: (1) energy catabolism and mitochondrial proteins; (2) chaperone proteins; and (3) cytoskeleton, exocytosis, and calcium. Changes in the expression of six proteins, identified by the 2D-MS proteomics procedure, were corroborated by a nanoliquid chromatography-mass spectrometry proteomics procedure (nLC-MS). Our results show that long-term starvation compromises essential functions of the brain related with energetic metabolism, synapsis, and the transmission of nervous impulse.

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Bayesian identification of protein differential expression in multi-group isobaric labelled mass spectrometry data

Statistical Applications in Genetics and Molecular Biology ◽

10.1515/sagmb-2012-0066 ◽

2014 ◽

Vol 13 (5) ◽

Cited By ~ 4

Author(s):

Howsun Jow ◽

Richard J. Boys ◽

Darren J. Wilkinson

Keyword(s):

Mass Spectrometry ◽

Simulated Data ◽

Differentially Expressed ◽

Mass Spectrometry Data ◽

Control Group ◽

Differentially Expressed Proteins ◽

Statistical Methodology ◽

Proteomic Data ◽

Bayesian Identification ◽

Multiple Groups

AbstractIn this paper we develop a Bayesian statistical inference approach to the unified analysis of isobaric labelled MS/MS proteomic data across multiple experiments. An explicit probabilistic model of the log-intensity of the isobaric labels’ reporter ions across multiple pre-defined groups and experiments is developed. This is then used to develop a full Bayesian statistical methodology for the identification of differentially expressed proteins, with respect to a control group, across multiple groups and experiments. This methodology is implemented and then evaluated on simulated data and on two model experimental datasets (for which the differentially expressed proteins are known) that use a TMT labelling protocol.

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