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https://www.readbyqxmd.com/read/28239971/characterization-of-n-methylated-amino-acids-by-gc-ms-after-ethyl-chloroformate-derivatization
#1
B Sudarshana Reddy, V Naresh Chary, P Pavankumar, S Prabhakar
Methylation is an essential metabolic process in the biological systems, and it is significant for several biological reactions in living organisms. Methylated compounds are known to be involved in most of the bodily functions, and some of them serve as biomarkers. Theoretically, all α-amino acids can be methylated, and it is possible to encounter them in most animal/plant samples. But the analytical data, especially the mass spectral data, are available only for a few of the methylated amino acids. Thus, it is essential to generate mass spectral data and to develop mass spectrometry methods for the identification of all possible methylated amino acids for future metabolomic studies...
August 2016: Journal of Mass Spectrometry: JMS
https://www.readbyqxmd.com/read/28237112/proteomic-profiling-of-de-novo-protein-synthesis-in-starvation-induced-autophagy-using-bioorthogonal-noncanonical-amino-acid-tagging
#2
J Zhang, J Wang, Y-M Lee, T-K Lim, Q Lin, H-M Shen
Autophagy is an intracellular degradation process activated by stress factors such as nutrient starvation to maintain cellular homeostasis. There is emerging evidence demonstrating that de novo protein synthesis is involved in the autophagic process. However, up-to-date characterizing of these de novo proteins is technically difficult. In this chapter, we describe a novel method to identify newly synthesized proteins during starvation-mediated autophagy by bioorthogonal noncanonical amino acid tagging (BONCAT), in conjunction with isobaric tagging for relative and absolute quantification (iTRAQ)-based quantitative proteomics...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28235584/proteomic-analysis-in-kidneys-of-atlantic-salmon-infected-with-aeromonas-salmonicida-by-itraq
#3
Peng-Fei Liu, Yishuai Du, Lingjie Meng, Xian Li, Ying Liu
Aeromonas salmonicida is a major etiologic agent which induces furunculosis and is globally harmful in salmonid and turbot cultures, especially in Atlantic salmon (Salmo salar) farming. In order to improve knowledge of its poorly understood pathogenesis, we utilized high-throughput proteomics to display differentially expressed proteins in the kidney of Atlantic salmon challenged with high and low infection dose of A. salmonicida at 7 and 14 days. In quantitative proteomic assays, isobaric tags for relative and absolute quantitation (iTRAQ) combined with 2D LC-MS/MS is emerging as a powerful methodology in the search for disease-specific targets and biomarkers...
February 21, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28230966/increasing-peak-capacity-in-non-targeted-omics-applications-by-combining-full-scan-field-asymmetric-waveform-ion-mobility-spectrometry-with-liquid-chromatography-mass-spectrometry
#4
Kayleigh L Arthur, Matthew A Turner, James C Reynolds, Colin S Creaser
Full scan field asymmetric waveform ion mobility spectrometry (FAIMS) combined with liquid chromatography and mass spectrometry (LC-FAIMS-MS) is shown to enhance peak capacity for omics applications. A miniaturized FAIMS device capable of rapid compensation field scanning has been incorporated into an ultra-high performance liquid chromatography (UHPLC) and time-of-flight (TOF) mass spectrometry analysis, allowing the acquisition of full scan FAIMS and MS nested data sets within the timescale of a UHPLC peak...
February 23, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28228353/isochoric-and-isobaric-freezing-of-fish-muscle
#5
Gabriel Năstase, Chenang Lyu, Gideon Ukpai, Alexandru Şerban, Boris Rubinsky
We have recently shown that, a living organism, which succumbs to freezing to -4 °C in an isobaric thermodynamic system (constant atmospheric pressure), can survive freezing to -4 °C in an isochoric thermodynamic system (constant volume). It is known that the mechanism of cell damage in an isobaric system is the freezing caused increase in extracellular osmolality, and, the consequent cell dehydration. An explanation for the observed survival during isochoric freezing is the thermodynamic modeling supported hypothesis that, in the isochoric frozen solution the extracellular osmolality is comparable to the cell intracellular osmolality...
February 20, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28228233/analyzing-complex-mixtures-of-drug-like-molecules-ion-mobility-as-an-adjunct-to-existing-liquid-chromatography-tandem-mass-spectrometry-methods
#6
Jasper Boschmans, Filip Lemière, Frank Sobott
The use of traveling wave ion mobility mass spectrometry (TWIMS) is evaluated in conjunction with, and as a possible alternative to, conventional LC-MS(/MS) methods for the separation and characterization of drug-like compounds and metabolites. As a model system we use an in vitro incubation mixture of the chemotherapeutic agent melphalan, which results in more than ten closely related hydrolysis products and chain-like oligomers. Ion mobility as a filtering tool results in the separation of ions of interest from interfering ions, based on charge state and shape/size...
February 14, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28224245/evaluation-of-ms-2-workflows-in-lc-q-orbitrap-for-pesticide-multi-residue-methods-in-fruits-and-vegetables
#7
Łukasz Rajski, María Del Mar Gómez Ramos, Amadeo R Fernández-Alba
LC-Q-Orbitrap efficiency was evaluated for pesticide multi-residue analysis by using three workflows involving simultaneous MS and MS(2) analysis. They were as follows: data-dependent MS(2) (dd-MS(2)), all-ion fragmentation (AIF) and variable data-independent analysis (vDIA). These MS(2) workflows were tested for the main method validation parameters such as detection and identification capabilities, repeatability, linear range and quantitation. QuEChER acetonitrile extracts (blanks and spiked with 166 pesticides) of 11 different fruits and vegetables were used for this evaluation...
February 21, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28222113/differentially-expressed-proteins-underlying-childhood-cortical-dysplasia-with-epilepsy-identified-by-itraq-proteomic-profiling
#8
Lu Qin, Xi Liu, Shiyong Liu, Yi Liu, Yixuan Yang, Hui Yang, Yangmei Chen, Lifen Chen
Cortical dysplasia accounts for at least 14% of epilepsy cases, and is mostly seen in children. However, the understanding of molecular mechanisms and pathogenesis underlying cortical dysplasia is limited. The aim of this cross-sectional study is to identify potential key molecules in the mechanisms of cortical dysplasia by screening the proteins expressed in brain tissues of childhood cortical dysplasia patients with epilepsy using isobaric tags for relative and absolute quantitation-based tandem mass spectrometry compared to controls, and several differentially expressed proteins that are not reported to be associated with cortical dysplasia previously were selected for validation using real-time polymerase chain reaction, immunoblotting and immunohistochemistry...
2017: PloS One
https://www.readbyqxmd.com/read/28221792/itraq-based-quantitative-proteomic-analysis-of-germinating-barley-under-ga-and-aba-treatments
#9
Yuqing Huang, Shengguan Cai, Jianbin Zeng, Dezhi Wu, Guoping Zhang
The degradation of starch in barley grains is a primary step of beer production. The addition of appropriate amount of GA promotes the production of fermentable sugars, beneficial to brewing industry. However, the response of proteomics in germinating barley to GA and ABA treatments is not thoroughly understood. In this study, iTRAQ (isobaric tags for relative and absolute quantitation) proteomics analysis was performed to illustrate the change of proteins in Tibetan wild barley XZ72 and XZ95 under GA and ABA treatments during germination...
February 21, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28221173/new-developments-in-transplant-proteomics
#10
Julie Ho, Patricia Hirt-Minkowski, John A Wilkins
PURPOSE OF REVIEW: Despite modern immunosuppression, renal allograft rejection remains a major contributor to graft loss. Novel biomarkers may help improve posttransplant outcomes through the early detection and treatment of rejection. Our objective is to provide an overview of proteomics, review recent discovery-based rejection studies, and explore innovative approaches in biomarker development. RECENT FINDINGS: Urine MMP7 was identified as a biomarker of subclinical and clinical rejection using two-dimensional liquid chromatography tandem-mass spectrometry (LC-MS/MS) and improved the overall diagnostic discrimination of urine CXCL10 : Cr alone for renal allograft inflammation...
February 17, 2017: Current Opinion in Nephrology and Hypertension
https://www.readbyqxmd.com/read/28220636/identification-of-candidate-biomarkers-for-the-prediction-of-gestational-diabetes-mellitus-in-the-early-stages-of-pregnancy-using-itraq-quantitative-proteomics
#11
Danqing Zhao, Liming Shen, Yan Wei, Jiaming Xie, Shuqiang Chen, Yi Liang, Youjiao Chen, Haorong Wu
PURPOSE: Gestational diabetes mellitus (GDM) is one of the most common medical problems of pregnancy. This study is designed to identify serum biomarkers which can predict the subsequent development of GDM at early stages. EXPERIMENTAL DESIGN: Maternal blood was obtained prospectively from pregnant women at 12-16 weeks of pregnancy. Among these, 30 women were subsequently diagnosed with GDM at 24 to 28 weeks and were selected as case studies along with 30 normoglycemic women as controls...
February 21, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28218834/unambiguous-identification-of-serine-and-threonine-pyrophosphorylation-using-neutral-loss-triggered-ethcd-mass-spectrometry
#12
Martin Penkert, Lisa M Yates, Michael Schuemann, David H Perlman, Dorothea Fiedler, Eberhard Krause
Tandem mass spectrometry (MS/MS) has emerged as the core technology for identification of posttranslational modifications (PTMs). Here, we report the mass spectrometry analysis of serine and threonine pyrophosphorylation, a protein modification that has eluded detection by conventional MS/MS methods. Analysis of a set of synthesized, site-specifically modified peptides by different fragmentation techniques shows that pyrophosphorylated peptides exhibit a characteristic neutral loss pattern of 98, 178 and 196 Da, which enables the distinction between isobaric pyro- and diphosphorylated peptides...
February 20, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28214264/identification-of-candidate-cerebrospinal-fluid-biomarkers-in-parkinsonism-using-quantitative-proteomics
#13
N K Magdalinou, A J Noyce, R Pinto, E Lindstrom, J Holmén-Larsson, M Holtta, K Blennow, H R Morris, T Skillbäck, T T Warner, A J Lees, I Pike, M Ward, H Zetterberg, J Gobom
INTRODUCTION: Neurodegenerative parkinsonian syndromes have significant clinical and pathological overlap, making early diagnosis difficult. Cerebrospinal fluid (CSF) biomarkers may aid the differentiation of these disorders, but other than α-synuclein and neurofilament light chain protein, which have limited diagnostic power, specific protein biomarkers remain elusive. OBJECTIVES: To study disease mechanisms and identify possible CSF diagnostic biomarkers through discovery proteomics, which discriminate parkinsonian syndromes from healthy controls...
January 31, 2017: Parkinsonism & related Disorders
https://www.readbyqxmd.com/read/28201904/relaxation-time-and-excess-entropy-in-viscous-liquids-electric-field-versus-temperature-as-control-parameter
#14
Ranko Richert
On the basis of adiabatic calorimetry data and results obtained from dielectric relaxation studies in the presence of a high static electric field, the effects of temperature and electric field induced changes of the excess entropy are compared for the same sample: supercooled cresolphthalein dimethylether. A field induced reduction of the excess entropy by 45 mJ K(-1) mol(-1) at constant temperature increases the structural relaxation time by 0.75%, while the same entropy change originating from lowering the temperature at constant field increases the time constant by 3...
February 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28197637/inhibition-of-fasn-suppresses-migration-invasion-and-growth-in-hepatoma-carcinoma-cells-by-deregulating-the-hif-1%C3%AE-igfbp1-pathway
#15
Jiaojiao Gong, Shasha Shen, Yixuan Yang, Si Qin, Lifan Huang, Hongmin Zhang, Ling Chen, Yaqin Chen, Shiying Li, Sha She, Min Yang, Hong Ren, Huaidong Hu
Hepatocellular carcinoma is the second most common cause of cancer-related deaths worldwide. Due to a high propensity to metastasize, active angiogenesis and rapid proliferation, recurrence and poor prognosis are major obstacles for treatment and cure of this disease. However, the detailed mechanisms of how fatty acid synthase (FASN) promotes migration, invasion and healing in tumor cells remain unclear. In the present study, the previous results that FASN was expressed higher in cancer samples than in non-cancerous samples, and influenced migration, invasion of hepatoma carcinoma cells, were verified by immunohistochemistry, tissue microarrays, Transwell assay and wound healing assay...
March 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28195392/relative-protein-quantification-and-accessible-biology-in-lung-tumor-proteomes-from-four-lc-ms-ms-discovery-platforms
#16
Paul A Stewart, Bin Fang, Robbert J C Slebos, Guolin Zhang, Adam L Borne, Katherine Fellows, Jamie K Teer, Y Ann Chen, Eric Welsh, Steven A Eschrich, Eric B Haura, John M Koomen
Discovery proteomics experiments include many options for sample preparation and mass spectrometry data acquisition, which are capable of creating datasets for quantifying thousands of proteins. To define a strategy that would produce a dataset with sufficient content while optimizing required resources, we compared 1) single sample liquid chromatography-tandem mass spectrometry (LC-MS/MS) with data dependent acquisition (DDA) to single sample LC-MS/MS with data independent acquisition (DIA) and 2) peptide fractionation with label-free quantification (LF) to isobaric labeling followed by peptide fractionation (TMT 6-plex)...
February 14, 2017: Proteomics
https://www.readbyqxmd.com/read/28194965/extensive-peptide-fractionation-and-y1-ion-based-interference-detection-method-for-enabling-accurate-quantification-by-isobaric-labeling-and-mass-spectrometry
#17
Mingming Niu, Ji-Hoon Cho, Kiran Kodali, Vishwajeeth Pagala, Anthony A High, Hong Wang, Zhiping Wu, Yuxin Li, Wenjian Bi, Hui Zhang, Xusheng Wang, Wei Zou, Junmin Peng
Isobaric labeling quantification by mass spectrometry (MS) has emerged as a powerful technology for multiplexed large-scale protein profiling, but measurement accuracy in complex mixtures is confounded by the interference from coisolated ions, resulting in ratio compression. Here we report that the ratio compression can be essentially resolved by the combination of pre-MS peptide fractionation, MS2-based interference detection, and post-MS computational interference correction. To recapitulate the complexity of biological samples, we pooled tandem mass tag (TMT)-labeled Escherichia coli peptides at 1:3:10 ratios and added in ∼20-fold more rat peptides as background, followed by the analysis of two-dimensional liquid chromatography (LC)-MS/MS...
February 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28193495/1%C3%AE-25-dihydroxyvitamin-d3-a-new-vitamin-d-metabolite-in-human-serum
#18
Steven Pauwels, Ivo Jans, Jaak Billen, Annemieke Heijboer, Annemieke Verstuyf, Geert Carmeliet, Chantal Mathieu, Miguel Maestro, Etienne Waelkens, Pieter Evenepoel, Roger Bouillon, Dirk Vanderschueren, Pieter Vermeersch
BACKGROUND: The measurement of 1α,25(OH)2D3 in human serum poses a true challenge as concentrations are very low and structurally similar metabolites can interfere. MATERIALS AND METHODS: During optimization of our in-house LC-MSMS method for serum 1α,25(OH)2D3 a previously co-eluting isobaric interference was separated. The isobar was identified as 1β,25(OH)2D3 by comparing retention time and fragmentation spectra to standards (other isobaric dihydroxylated vitamin D3 analogs)...
February 11, 2017: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28191739/itraq-based-quantitative-proteomic-analysis-of-wheat-roots-in-response-to-salt-stress
#19
Qiyan Jiang, Xiaojuan Li, Fengjuan Niu, Xianjun Sun, Zheng Hu, Hui Zhang
Salinity is a major abiotic stress that affects plant growth and development. Plant roots are the sites of salt uptake. Here, an isobaric tag for a relative and absolute quantitation (iTRAQ)-based proteomic technique was employed to identify the differentially expressed proteins (DEPs) from seedling roots of the salt-tolerant genotype Han 12 and the salt-sensitive genotype Jimai 19 in response to salt treatment. A total of 121 NaCl-responsive DEPs were observed in Han 12 and Jimai 19. The main DEPs were ubiquitination-related proteins, transcription factors, pathogen-related proteins, membrane intrinsic protein transporters and antioxidant enzymes, which may work together to obtain cellular homeostasis in roots and determine the overall salt tolerance of different wheat varieties in response to salt stress...
February 13, 2017: Proteomics
https://www.readbyqxmd.com/read/28190699/correcting-false-positive-medium-chain-acyl-coa-dehydrogenase-deficiency-results-from-newborn-screening-synthesis-purification-and-standardization-of-branched-chain-c8-acylcarnitines-for-use-in-their-selective-and-accurate-absolute-quantitation-by-uhplc-ms
#20
Paul E Minkler, Maria S K Stoll, Stephen T Ingalls, Charles L Hoppel
While selectively quantifying acylcarnitines in thousands of patient samples using UHPLC-MS/MS, we have occasionally observed unidentified branched-chain C8 acylcarnitines. Such observations are not possible using tandem MS methods, which generate pseudo-quantitative acylcarnitine "profiles". Since these "profiles" select for mass alone, they cannot distinguish authentic signal from isobaric and isomeric interferences. For example, some of the samples containing branched-chain C8 acylcarnitines were, in fact, expanded newborn screening false positive "profiles" for medium-chain acyl-CoA dehydrogenase deficiency (MCADD)...
February 8, 2017: Molecular Genetics and Metabolism
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