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Journal of Proteome Research

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https://www.readbyqxmd.com/read/28820946/proteogenomic-investigation-of-strain-variation-in-clinical-mycobacterium-tuberculosis-isolates
#1
Tiaan Heunis, Anzaan Dippenaar, Robin M Warren, Paul D van Helden, Ruben G van der Merwe, Nicolaas C Gey van Pittius, Arnab Pain, Samantha L Sampson, David L Tabb
Mycobacterium tuberculosis consists of a large number of different strains that display unique virulence characteristics. Whole-genome sequencing has revealed substantial genetic diversity among clinical M. tuberculosis isolates, and elucidating the phenotypic variation encoded by this genetic diversity will be of utmost importance to fully understand M. tuberculosis biology and pathogenicity. In this study we integrated whole-genome sequencing and mass spectrometry (GeLC-MS/MS) to reveal strain-specific characteristics in the proteomes of two clinical M...
August 18, 2017: Journal of Proteome Research
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...
August 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28753293/acid-salt-ph-gradient-improved-resolution-and-sensitivity-in-proteomics-study-using-2d-scx-rp-lc-ms
#3
Ming-Zhi Zhu, Na Li, Yi-Tong Wang, Ning Liu, Ming-Quan Guo, Bao-Qing Sun, Hua Zhou, Liang Liu, Jian-Lin Wu
The usage of strong cation exchange (SCX) chromatography in proteomics is limited by its poor resolution and nonspecific hydrophobic interactions with peptides, which lead to peptide overlap across fractions and change of peptide retention, respectively. The application of high concentration of salt (up to 1000 mM) in SCX also restricted its use in online 2D SCX-RP LC. In the present research, we first exploited the chromatographic ability of online 2D SCX-RP LC by combination of acid, salt, and pH gradient, three relatively independent modes of eluting peptides from SCX column...
August 17, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28753027/-1-h-nmr-metabolic-profiling-of-earthworm-eisenia-fetida-coelomic-fluid-coelomocytes-and-tissue-identification-of-a-new-metabolite-malylglutamate
#4
Corey M Griffith, Preston B Williams, Luzineide W Tinoco, Meredith M Dinges, Yinsheng Wang, Cynthia K Larive
Earthworm metabolism is recognized as a useful tool for monitoring environmental insults and measuring ecotoxicity, yet extensive earthworm metabolic profiling using (1)H nuclear magnetic resonance (NMR) spectroscopy has been limited in scope. This study aims to expand the embedded metabolic material in earthworm coelomic fluid, coelomocytes, and tissue to aid systems toxicology research. Fifty-nine metabolites within Eisenia fetida were identified, with 47 detected in coelomic fluid, 41 in coelomocytes, and 54 in whole-worm samples and tissue extracts...
August 16, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28753016/high-throughput-metabolomics-for-discovering-potential-metabolite-biomarkers-and-metabolic-mechanism-from-the-appswe-ps1de9-transgenic-model-of-alzheimer-s-disease
#5
Jingbo Yu, Ling Kong, Aihua Zhang, Ying Han, Zhidong Liu, Hui Sun, Liang Liu, Xijun Wang
Alzheimer's disease (AD), a neurodegenerative disorder, is the major form of dementia. As AD is an irreversible disease, it is necessary to focus on earlier intervention. However, the potential biomarkers of preclinical AD are still not clear. In this study, urinary metabolomics based on ultra-high-performance liquid chromatography coupled with quadruple time-of-flight mass spectrometry was performed for delineating the metabolic changes and potential early biomarkers in APPswe/PS1dE9 (APP/PS1) transgenic mice...
August 16, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28745058/impact-of-influenza-a-virus-infection-on-the-proteomes-of-human-bronchoepithelial-cells-from-different-donors
#6
Samuel T Mindaye, Natalia A Ilyushina, Giovanna Fantoni, Michail A Alterman, Raymond P Donnelly, Maryna C Eichelberger
Susceptibility to influenza A virus is determined by a balance of viral and host factors. The genetic background of the host contributes to the severity of disease, but the influenza-related proteomes of cells from different individuals have not been compared. We used high-resolution mass spectrometry to identify proteins in normal human bronchial epithelial (NHBE) cells isolated from three different donors. Infection of each NHBE cell culture with influenza A/California/07/2009 (H1N1) resulted in expression of viral proteins and a variety of host proteins, including interferons, interferon-stimulated genes, and secreted chemokines/cytokines...
August 16, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28587463/lipidomics-profiling-of-human-adipose-tissue-identifies-a-pattern-of-lipids-associated-with-fish-oil-supplementation
#7
Elizabeth G Stanley, Benjamin J Jenkins, Celia G Walker, Albert Koulman, Lucy Browning, Annette L West, Philip C Calder, Susan A Jebb, Julian L Griffin
To understand the interaction between diet and health, biomarkers that accurately reflect consumption of foods of perceived health relevance are needed. The aim of this investigation was to use direct infusion-mass spectrometry (DI-MS) lipidomics to determine the effects of fish oil supplementation on lipid profiles of human adipose tissue. Adipose tissue samples from an n-3 polyunsaturated fatty acid (PUFA) supplementation study (n = 66) were analyzed to compare the pattern following supplementation equivalent to zero or four portions of oily fish per week...
August 16, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28810742/determination-of-rate-limiting-factor-for-formation-of-beta-catenin-destruction-complexes-using-absolute-protein-quantification
#8
Masashi Kitazawa, Tomohisa Hatta, Koji Ogawa, Eriko Fukuda, Naoki Goshima, Tohru Natsume
Wnt/β-catenin signaling plays important roles in both ontogenesis and development. In the absence of a Wnt stimulus, β-catenin is degraded by a multiprotein "destruction complex" that includes Axin, APC, GSK3B, and FBXW11. Although the key molecules required for transducing Wnt signals have been identified, a quantitative understanding of this pathway has been lacking. Here, we calculated the absolute number of β-catenin destruction complexes by absolute protein quantification using LC-MS/MS. Similar amounts of destruction complex-constituting proteins and β-catenin interacted, and the number of destruction complexes was calculated to be about 1,468 molecules/cell...
August 15, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28810121/comparative-proteomic-and-transcriptomic-analysis-of-follistatin-induced-skeletal-muscle-hypertrophy
#9
Caroline Barbé, Fabrice Bray, Marine Gueugneau, Stéphanie Devassine, Pascale Lause, Caroline Tokarski, Christian Rolando, Jean-Paul Thissen
Skeletal muscle, the most abundant body's tissue, plays vital roles in locomotion and metabolism. Myostatin is a negative regulator of skeletal muscle mass. In addition to increase muscle mass, Myostatin inhibition impacts on muscle contractility and energy metabolism. To decipher the mechanisms of action of the Myostatin inhibitors, we used proteomic and transcriptomic approaches to investigate the changes induced in skeletal muscles of transgenic mice overexpressing Follistatin, a physiological Myostatin inhibitor...
August 15, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28809572/antigen-specific-gut-inflammation-and-systemic-immune-responses-induced-by-pro-longing-wheat-gluten-sensitization-in-balb-c-murine-model
#10
Vijaykrishnaraj M, Mohan Kumar Bv, Muthukumar Sp, Nawneet K Kurrey, Pichan Prabhasankar
Gluten-related diseases such as wheat allergy, celiac disease, and gluten intolerance are widespread in the globe to genetically pre-disposed individuals. The present study aims to develop wheat-gluten induced BALB/c murine model for addressing wheat-gluten related disorders by sensitizing the wheat gluten through the route of intraperitoneal and oral challenge in prolonged days. During the sensitization, the sera were collected for specific anti-gliadin antibodies response and pro-inflammatory markers quantification...
August 15, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28809118/glucose-limitation-alters-glutamine-metabolism-in-muc1-overexpressing-pancreatic-cancer-cells
#11
Teklab Gebregiworgis, Vinee Purohit, Surendra K Shukla, Saber Tadros, Nina V Chaika, Jaime Abrego, Scott E Mulder, Venugopal Gunda, Pankaj K Singh, Robert Powers
Pancreatic cancer cells overexpressing MUC1 rely on aerobic glycolysis and, correspondingly, are dependent on glucose for survival. Our NMR metabolomics comparative analysis of control (S2-013.Neo) and MUC1-overexpressing (S2-013.MUC1) cells demonstrate that MUC1 reprograms glutamine metabolism upon glucose limitation. The observed alteration in glutamine metabolism under glucose limitation accompanied with a relative decrease in the proliferation of MUC1-overexpressing cells compared to steady state conditions...
August 15, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28799767/a-comprehensive-metabolomics-study-to-assess-longitudinal-biochemical-changes-and-potential-early-biomarkers-in-nod-mice-that-progress-to-diabetes
#12
Peter Buchwald, Alejandro Tamayo-Garcia, Sivapriya Ramamoorthy, Marta Garcia-Contreras, Armando J Mendez, Camillo Ricordi
A global non-targeted longitudinal metabolomics study was carried out in male and female NOD mice to characterize the time-profile of the changes in the metabolic signature caused by onset of type 1 diabetes (T1D) and identify possible early biomarkers in T1D progressors. Metabolomics profiling of samples collected at five different time-points identified 676 and 706 biochemicals in blood and feces, respectively. Several metabolites were expressed at significantly different levels in progressors at all time-points, and their proportion increased strongly following onset of hyperglycemia...
August 11, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28799334/the-impact-of-commonly-used-alkylating-agents-on-artefactual-peptide-modification
#13
Peter G Hains, Phillip J Robinson
Iodoacetamide is by far the most commonly used agent for alkylation of cysteine during sample preparation for proteomics. An alternative, 2-chloroacetamide, has been recently suggested to reduce the alkylation of residues other than cysteine, such as the N-terminus, Asp, Glu, Lys, Ser, Thr and Tyr. Here, we show that although 2-chloroacetamide reduces the level of off-target alkylation, it exhibits a range of adverse effects. The most significant of these was methionine oxidation, which increases to a maximum of 40% of all Met containing peptides compared to 2-5% with iodoacetamide...
August 11, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28795575/accurate-identification-of-unknown-and-known-metabolic-mixture-components-by-combining-3d-nmr-with-ft-icr-ms-ms
#14
Cheng Wang, Lidong He, Dawei Li, Lei Bruschweiler-Li, Alan G Marshall, Rafael Bruschweiler
Metabolite identification in metabolomics samples is a key step that critically impacts downstream analysis. We recently introduced the SUMMIT NMR/MS hybrid approach for the identification of the molecular structure of unknown metabolites, based on the combination of NMR, mass spectrometry (MS), and combinatorial cheminformatics. Here, we demonstrate the feasibility of the approach for an untargeted analysis of both a model mixture and E. coli cell lysate, based on 2D/3D NMR experiments in combination with FT-ICR MS and MS/MS data...
August 10, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28792770/proteomic-analysis-of-brain-and-cerebrospinal-fluid-from-the-three-major-forms-of-neuronal-ceroid-lipofuscinosis-reveals-potential-biomarkers
#15
David E Sleat, Abla Tannous, Istvan Sohar, Jennifer A Wiseman, Haiyan Zheng, Meiqian Qian, Caifeng Zhou, Winnie Xin, Rosemary Barone, Katherine B Sims, Dirk F Moore, Peter Lobel
Clinical trials have been conducted for the neuronal ceroid lipofuscinoses (NCLs), a group of neurodegenerative lysosomal diseases that primarily affect children. While clinical rating systems will evaluate long-term efficacy, biomarkers to measure short-term response to treatment would be extremely valuable. To identify candidate biomarkers, we analyzed autopsy brain and matching CSF samples from controls and three genetically distinct NCLs due to deficiencies in palmitoyl protein thioesterase 1 (CLN1 disease), tripeptidyl peptidase 1 (CLN2 disease) and CLN3 protein (CLN3 disease)...
August 9, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28791867/evolution-of-newborns-urinary-metabolomic-profiles-according-to-age-and-growth
#16
Aurélien Scalabre, Elodie Jobard, Delphine Demède, Ségolène Gaillard, Clément Pontoizeau, Pierre Mouriquand, Bénédicte Elena-Herrmann, Pierre-Yves Mure
Improving the management of neonatal diseases and prevention of chronic diseases in adulthood requires a better comprehension of the complex maturational processes associated with newborns development. Urine-based metabolomic studies play a promising role in the fields of pediatrics and neonatology, relying on simple and non-invasive collection procedures while integrating a variety of factors such as genotype, nutritional state, lifestyle and diseases. Here, we investigate the influence of age, weight, height and gender on the urine metabolome during the first 4 months of life...
August 9, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28786289/profiling-of-acylcarnitines-in-first-episode-psychosis-before-and-after-antipsychotic-treatment
#17
Kärt Kriisa, Liisa Leppik, Roman Balõtšev, Aigar Ottas, Ursel Soomets, Kati Koido, Vallo Volke, Jürgen Innos, Liina Haring, Eero Vasar, Mihkel Zilmer
AIM: Acylcarnitines (ACs) have been shown to have a potential to activate pro-inflammatory signalling pathways and to foster the development of insulin resistance. The first task of the current study was to study the full list of ACs (from C2 to C18) in first episode psychosis (FEP) patients before and after antipsychotic treatment. The second task was to relate ACs to inflammatory and metabolic biomarkers established in the same patient cohort as in our previous studies. METHODS: Serum level of ACs were determined with the AbsoluteIDQ™ p180 kit (BIOCRATES Life Sciences AG, Innsbruck, Austria) using the flow injection analysis tandem mass spectrometry ([FIA]-MS/MS) as well as liquid chromatography ([LC]-MS/MS) technique...
August 8, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28738681/optimizing-high-resolution-mass-spectrometry-for-the-identification-of-low-abundance-post-translational-modifications-of-intact-proteins
#18
Lisa E Kilpatrick, Eric L Kilpatrick
Intact protein analysis by liquid chromatography-mass spectrometry (LC-MS) is now possible due to the improved capabilities of mass spectrometers yielding greater resolution, mass accuracy, and extended mass ranges. Concurrent measurement of post-translational modifications (PTMs) during LC-MS of intact proteins is advantageous while monitoring critical proteoform status, such as for clinical samples or during production of reference materials. However, difficulties exist for PTM identification when the protein is large or contains multiple modification sites...
August 8, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28738677/quantitation-of-87-proteins-by-nlc-mrm-ms-in-human-plasma-workflow-for-large-scale-analysis-of-biobank-samples
#19
Melinda Rezeli, Karin Sjödin, Henrik Lindberg, Olof Gidlöf, Bertil Lindahl, Tomas Jernberg, Jonas Spaak, David Erlinge, György Marko-Varga
A multiple reaction monitoring (MRM) assay was developed for precise quantitation of 87 plasma proteins including the three isoforms of apolipoprotein E (APOE) associated with cardiovascular diseases using nanoscale liquid chromatography separation and stable isotope dilution strategy. The analytical performance of the assay was evaluated and we found an average technical variation of 4.7% in 4-5 orders of magnitude dynamic range (≈0.2 mg/L to 4.5 g/L) from whole plasma digest. Here, we report a complete workflow, including sample processing adapted to 96-well plate format and normalization strategy for large-scale studies...
August 8, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28737031/ubiquitin-chain-enrichment-middle-down-mass-spectrometry-ubichem-ms-reveals-cell-cycle-dependent-formation-of-lys11-lys48-branched-ubiquitin-chains
#20
Ambar S J B Rana, Ying Ge, Eric R Strieter
The dynamics of cellular signaling events are tightly regulated by a diverse set of ubiquitin chains. Recent work has suggested that branched ubiquitin chains composed of Lys11 and Lys48 isopeptide linkages play a critical role in regulating cell cycle progression. Yet, endogenous Lys11/Lys48 branched chains could not be detected. By combining a Lys11 linkage specific antibody with high-resolution middle-down mass spectrometry (an approach termed UbiChEM-MS) we sought to identify endogenous Lys11/Lys48 branched ubiquitin chains in cells...
August 7, 2017: Journal of Proteome Research
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