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proteomics methods

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https://www.readbyqxmd.com/read/28746408/microwave-magnetic-proteomics-of-macrophages-from-patients-with-hiv-associated-cognitive-impairment
#1
Yisel M Cantres-Rosario, Frances M Acevedo-Mariani, Juliana Pérez-Laspiur, William E Haskins, Marines Plaud, Yadira M Cantres-Rosario, Richard Skolasky, Israel Méndez-Bermúdez, Valerie Wojna, Loyda M Meléndez
OBJECTIVE: HIV-infected monocytes can infiltrate the blood brain barrier as differentiated macrophages to the central nervous system, becoming the primary source of viral and cellular neurotoxins. The final outcome is HIV-associated cognitive impairment (HACI), which remain prevalent today, possibly due to the longer life-span of the patients treated with combined anti-retroviral therapy. Our main goal was to characterize the proteome of monocyte-derived macrophages (MDM) from HACI patients, and its association with their cognitive status, to find novel targets for therapy...
2017: PloS One
https://www.readbyqxmd.com/read/28745510/statistical-models-for-the-analysis-of-isobaric-tags-multiplexed-quantitative-proteomics
#2
Gina D'Angelo, Raghothama Chaerkady, Wen Yu, Deniz Baycin Hizal, Sonja Hess, Wei Zhao, Kristen Lekstrom, Xiang Guo, Wendy I White, Lorin Roskos, Michael A Bowen, Harry Yang
Mass spectrometry is being used to identify protein biomarkers that can facilitate development of drug treatment. Mass spectrometry based labeling proteomic experiments result in complex proteomic data that is hierarchical in nature often with small sample size studies. The generalized linear model (GLM) is the most popular approach in proteomics to compare protein abundances between groups. However, GLM does not address all the complexities of proteomics data such as repeated measures and variance heterogeneity...
July 26, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28745017/activation-of-engineered-protein-tyrosine-phosphatases-with-the-biarsenical-compound-ascy3-edt2
#3
Wai Cheung Chan, Gregory S Knowlton, Anthony C Bishop
Methods for activating signaling enzymes hold significant potential for the study of cellular signal transduction. Here we present a strategy for engineering chemically activatable protein tyrosine phosphatases (actPTPs). To generate actPTP1B, we introduced three cysteine point mutations in the enzyme's WPD loop. Biarsenical compounds were screened for the capability to bind actPTP1B's WPD loop and increase its phosphatase activity. We identified AsCy3-EDT2 as a robust activator that selectively targets actPTP1B in proteomic mixtures and intact cells...
July 25, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28742856/fit-for-genomic-and-proteomic-purposes-sampling-the-fitness-of-nucleic-acid-and-protein-derivatives-from-formalin-fixed-paraffin-embedded-tissue
#4
Anna Yakovleva, Jordan L Plieskatt, Sarah Jensen, Razan Humeida, Jonathan Lang, Guangzhao Li, Paige Bracci, Sylvia Silver, Jeffrey Michael Bethony
The demand for nucleic acid and protein derivatives from formalin-fixed paraffin-embedded (FFPE) tissue has greatly increased due to advances in extraction and purification methods, making these derivatives available for numerous genomic and proteomic platforms. Previously, DNA, RNA, microRNA (miRNA), or protein derived from FFPE tissue blocks were considered "unfit" for such platforms, as the process of tissue immobilization by FFPE resulted in cross-linked, fragmented, and chemically modified macromolecules...
2017: PloS One
https://www.readbyqxmd.com/read/28742267/profiling-the-effects-of-short-time-course-cold-ischemia-on-tumor-protein-phosphorylation-using-a-bayesian-approach
#5
You Wu, Jeremy Gaskins, Maiying Kong, Susmita Datta
Phosphorylated proteins provide insight into tumor etiology and are used as diagnostic, prognostic, and therapeutic markers of complex diseases. However, pre-analytic variations, such as freezing delay after biopsy acquisition, often occur in real hospital settings and potentially lead to inaccurate results. The objective of this work is to develop statistical methodology to assess the stability of phosphorylated proteins under short-time cold ischemia. We consider a hierarchical model to determine if phosphorylation abundance of a protein at a particular phosphorylation site remains constant or not during cold ischemia...
July 25, 2017: Biometrics
https://www.readbyqxmd.com/read/28742213/derivatization-agents-for-electrochemical-detection-in-amino-acid-peptide-and-protein-separations-the-hidden-electrochemistry
#6
REVIEW
Tania Sierra, Agustin G Crevillen, Alberto Escarpa
In proteomics and clinical analysis, LIF and MS are the most used detectors coupled to separation techniques. MS offers good sensitivity and analyte identification ability but, as counterbalance, it is expensive and it needed background electrolytes compatible with mass spectrometers. LIF detection offers the highest sensitivity but, in general, proteins, peptides and amino acids are not fluorescents so it is necessary the use of fluorescence tags. This fact hindered the potential sensitivity of LIF detection due to the difficulty of labeling analytes at extremely low concentrations...
July 25, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28742153/reconstructing-the-regulatory-circuit-of-cell-fate-determination-in-yeast-mating-response
#7
Bin Shao, Haiyu Yuan, Rongfei Zhang, Xuan Wang, Shuwen Zhang, Qi Ouyang, Nan Hao, Chunxiong Luo
Massive technological advances enabled high-throughput measurements of proteomic changes in biological processes. However, retrieving biological insights from large-scale protein dynamics data remains a challenging task. Here we used the mating differentiation in yeast Saccharomyces cerevisiae as a model and developed integrated experimental and computational approaches to analyze the proteomic dynamics during the process of cell fate determination. When exposed to a high dose of mating pheromone, the yeast cell undergoes growth arrest and forms a shmoo-like morphology; however, at intermediate doses, chemotropic elongated growth is initialized...
July 24, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28742123/molecular-and-maldi-tof-identification-of-ticks-and-tick-associated-bacteria-in-mali
#8
Adama Zan Diarra, Lionel Almeras, Maureen Laroche, Jean-Michel Berenger, Abdoulaye K Koné, Zakaria Bocoum, Abdoulaye Dabo, Ogobara Doumbo, Didier Raoult, Philippe Parola
Ticks are considered the second vector of human and animal diseases after mosquitoes. Therefore, identification of ticks and associated pathogens is an important step in the management of these vectors. In recent years, mass spectrometry of the laser disorder / matrix assisted ionization (MALDI-TOF MS) has been reported as a promising method for the identification of arthropods including ticks. The objective of this study was to improve the conditions for the preparation of tick samples for their identification by MALDI-TOF MS from field-collected ethanol-stored Malian samples and to evaluate the capacity of this technology to distinguish infected and uninfected ticks...
July 24, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28741358/combining-de-novo-peptide-sequencing-algorithms-a-synergistic-approach-to-boost-both-identifications-and-confidence-in-bottom-up-proteomics
#9
Bernhard Blank-Landeshammer, Laxmikanth Kollipara, Karsten Biß, Markus Pfenninger, Sebastian Malchow, Konstantin Shuvaev, René P Zahedi, Albert Sickmann
Complex mass spectrometry based proteomics datasets are mostly analyzed by protein database-searches. While this approach performs considerably well for sequenced organisms, direct inference of peptide sequences from tandem mass spectra, i.e. de novo peptide sequencing, oftentimes is the only way to obtain information when protein databases are absent. However, available algorithms suffer from drawbacks such as lack of validation and often high rates of false positive hits (FP). Here we present a simple method of combining results from commonly available de novo peptide sequencing algorithms, which in conjunction with minor tweaks in data acquisition ensues lower empirical FDR compared to the analysis using single algorithms...
July 25, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28741221/optimization-and-application-of-a-biotinylation-method-for-quantification-of-plasma-membrane-expression-of-transporters-in-cells
#10
Vineet Kumar, Tot Bui Nguyen, Beáta Tóth, Viktoria Juhasz, Jashvant D Unadkat
Quantitative proteomics, using LC-MS/MS, is increasingly used to quantify drug transporters present in tissues and cells. Most of these investigations quantify total transporter expression in the cells by utilizing a total membrane fraction, not only the plasma membrane. Here, we report development and optimization of a biotinylation method to quantify protein expression of transporters in the plasma membrane of cells. The Pierce cell surface isolation protocol was optimized for plasma membrane isolation. Incubation of OATP1B1-expressing CHO cells with 0...
July 24, 2017: AAPS Journal
https://www.readbyqxmd.com/read/28738651/recent-advances-in-sample-pre-treatment-for-emerging-methods-in-proteomic-analysis
#11
María Ramos-Payán, Juan A Ocaña-González, Rut M Fernández-Torres, Santiago Maspoch, Miguel Ángel Bello-López
The objective of proteomics is the study of proteins (including their structure elucidation, the characterization of their role in biochemical process, the detection and identification of anomalous modifications in their structures and behavior, etc.) from both a qualitative and quantitative point of view. These studies have to face several difficulties as (a) the intrinsic complexity of protein molecules, (b) the low concentrations of the studied proteins, (c) the complexity of the biological samples (which could lead to interferences from the components of these matrixes), etc...
November 1, 2017: Talanta
https://www.readbyqxmd.com/read/28738625/the-screening-of-organic-matter-in-mineral-and-tap-water-by-uhplc-hrms
#12
Marcos A S Ribeiro, Michael Murgu, Valquíria de Moraes Silva, Alexandra C H F Sawaya, Leomara Floriano Ribeiro, Andre Justi, Eduardo C Meurer
It is highly desirable to screen for a large variety of organic compounds in water. Ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS) can analyse semi-polar to polar organic compounds in tap and mineral water. The use of UHPLC-HRMS is well consolidated for lipidomic, metabolomic and proteomic studies; based on the detection of a very large number of compounds of a variety of organic functions. Water analysis is usually performed by gas chromatography -mass spectrometry (GC-MS) techniques that are efficient for volatile organic compounds...
November 1, 2017: Talanta
https://www.readbyqxmd.com/read/28738271/heterogeneous-photocatalysis-of-tris-2-chloroethyl-phosphate-by-uv-tio2-degradation-products-and-impacts-on-bacterial-proteome
#13
Jinshao Ye, Juan Liu, Chongshu Li, Pulin Zhou, Shuang Wu, Huase Ou
The widespread, persistent and toxic organophosphorus esters (OPEs) have become one category of emerging environmental contaminants. Thus, it is in urgent need to develop a cost-effective and safe treatment technology for OPEs control. The current study is a comprehensive attempt to use UV/TiO2 heterogeneous photocatalysis for the degradation of a water dissolved OPEs, tris(2-chloroethyl) phosphate (TCEP). A pseudo-first order degradation reaction with a kobs of 0.3167 min(-1) was observed, while hydroxyl radical may be the dominating reactive oxidative species...
July 18, 2017: Water Research
https://www.readbyqxmd.com/read/28737240/in-gel-and-offgel-based-proteomic-approach-for-authentication-of-meat-species-from-minced-meat-and-meat-products
#14
Basappa M Naveena, Deepak S Jagadeesh, Veeranna Kamuni, Muthukumar M, Vinayak V Kulkarni, Kiran M, Srikanth Rapole
BACKGROUND: Fraudulent mislabelling of processed meat products on global scale which could not be detected using conventional techniques demand for sensitive, robust and accurate methods of meat authentication to ensure food safety and public health. In the present study, we developed in-gel (2-dimensional gel electrophoresis, 2DE) and OFFGEL-based proteomic method for authenticating raw and cooked water buffalo (Bubalus bubalis), sheep (Ovis aries) and goat (Caprus hircus) meat and their mixes...
July 24, 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/28736082/differential-proteome-expression-analysis-of-androgen-dependent-and-independent-pathways-in-lncap-prostate-cancer-cells
#15
Seho Cha, Dong Hoon Shin, Jun Ryeong Seok, Jae Kyung Myung
Prostate cancer (PC) is one of the leading causes of cancer death in men. It commonly develops in older males, but the number of younger men diagnosed with the disease has increased in recent years. Hormone therapies, such as chemical and surgical methods that inhibit androgen synthesis or androgen receptor (AR) activation, have been used for advanced disease. However, castration-resistant PC (CRPC), which exhibits androgen-independent mechanisms for activating AR, develops after a few years of such treatment and no therapy is available...
July 20, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/28735397/global-proteomic-profiling-and-identification-of-stress-responsive-proteins-using-two-dimensional-gel-electrophoresis
#16
Pragya Barua, Dipak Gayen, Nilesh Vikram Lande, Subhra Chakraborty, Niranjan Chakraborty
Global proteome profiling is a direct representation of the protein set in an organism, organ, tissues, or an organelle. One of the main objectives of proteomic analysis is the comparison and relative quantitation of proteins under a defined set of conditions. Two-dimensional gel electrophoresis (2-DE) has gained prominence over the last 4 decades for successfully aiding differential proteomics, providing visual confirmation of changes in protein abundance, which otherwise cannot be predicted from genome analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28735396/isolation-of-polysomal-rna-for-analyzing-stress-responsive-genes-regulated-at-the-translational-level-in-plants
#17
Yong-Fang Li, Ramamurthy Mahalingam, Ramanjulu Sunkar
Alteration of gene expression is an essential mechanism, which allows plants to respond and adapt to adverse environmental conditions. Transcriptome and proteome analyses in plants exposed to abiotic stresses revealed that protein levels are not correlated with the changes in corresponding mRNAs, indicating regulation at translational level is another major regulator for gene expression. Analysis of translatome, which refers to all mRNAs associated with ribosomes, thus has the potential to bridge the gap between transcriptome and proteome...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28735093/stable-isotope-labeling-by-fatty-acids-in-cell-culture-silfac-coupled-with-isotope-pattern-dependent-mass-spectrometry-for-global-screening-of-lipid-hydroperoxide-mediated-protein-modifications
#18
Ryo Takahashi, Shuhei Fujioka, Tomoyuki Oe, Seon Hwa Lee
Lipid hydroperoxide-mediated modifications of proteins are receiving increasing attention because of their possible involvement in various degenerative diseases. These biological effects are attributed to the ability of lipid peroxidation-derived aldehydes to react with the nucleophilic sites of proteins. Here we describe a methodology involving metabolic labeling coupled with mass spectrometry-based proteomic analysis that enables global screening of lipid hydroperoxide-mediated protein modifications in a cell system...
July 19, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28734369/systematic-comparison-of-exosomal-proteomes-from-human-saliva-and-serum-for-the-detection-of-lung-cancer
#19
Yan Sun, Sha Liu, Zhi Qiao, Zhi Shang, Zhijun Xia, Xiaomin Niu, Liqiang Qian, Yan Zhang, Liuyin Fan, Cheng-Xi Cao, Hua Xiao
Circulating tumor exosomes harbor plenty of cancer biological information, which have emerged as promising targets for cancer early detection and diagnosis. Human serum and saliva are unique diagnostic body fluids, which contain numerous circulating exosomes. It is necessary to establish standardized isolation method and compare their proteome profiling for translational medicine. High abundant proteins in these body fluids were removed before exosomes isolation and obtained exosomes were further confirmed by morphology analysis and surface biomarker test...
August 22, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28734361/preparation-of-intact-mitochondria-using-free-flow-isoelectric-focusing-with-post-ph-gradient-sample-injection-for-morphological-functional-and-proteomics-studies
#20
Yu-Chen He, Fan-Zhi Kong, Liu-Yin Fan, Jane Y Wu, Xiao-Ping Liu, Jun Li, Yan Sun, Qiang Zhang, Ying Yang, Xue-Jing Wu, Hua Xiao, Cheng-Xi Cao
Mitochondria play essential roles in both energy metabolism and cell signaling, which are critical for cell survival. Although significant efforts have been invested in understanding mitochondrial biology, methods for intact mitochondria preparation are technically challenging and remain to be improved. New methods for heterogeneous mitochondria purification will therefore boost our understanding on their physiological and biophysical properties. Herein, we developed a novel recycling free-flow isoelectric focusing (RFFIEF) with post-pH gradient sample injection (post-PGSI) for preparative separation of mitochondria...
August 22, 2017: Analytica Chimica Acta
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