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Analytical Chemistry

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https://www.readbyqxmd.com/read/28914531/systems-level-annotation-of-a-metabolomics-data-set-reduces-25%C3%A2-000-features-to-fewer-than-1000-unique-metabolites
#1
Nathaniel G Mahieu, Gary J Patti
When using liquid chromatography/mass spectrometry (LC/MS) to perform untargeted metabolomics, it is now routine to detect tens of thousands of features from biological samples. Poor understanding of the data, however, has complicated interpretation and masked the number of unique metabolites actually being measured in an experiment. Here we place an upper bound on the number of unique metabolites detected in Escherichia coli samples analyzed with one untargeted metabolomics method. We first group multiple features arising from the same analyte, which we call "degenerate features", using a context-driven annotation approach...
September 15, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28911227/a-fluorescence-assay-for-ribonuclease-h-based-on-non-labeled-substrate-and-dnazyme-assisted-cascade-amplification
#2
Lanbo Wang, Hongyan Zhou, Bin Liu, Chuan Zhao, Jialong Fan, Wei Wang, Chunyi Tong
As a highly conserved damage repair protein, RNase H can specifically hydrolyze RNA in DNA-RNA chimeric strands. DNAzyme, a synthetic single-stranded DNA consisting of binding and catalytic sites, can cleave RNA in the presence of cofactors. In this study, we establish a highly sensitive RNase H assay assisted with DNAzyme's cleavage property. A DNA-RNA chimeric strand, which contains DNAzyme sequences, is used as the hydrolysis substrate of RNase H. The RNase H hydrolysis of the chimeric substrate results in the release of DNAzyme...
September 15, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28911223/direct-sampling-and-analysis-of-atmospheric-particulate-organic-matter-by-proton-transfer-reaction-mass-spectrometry
#3
Markus Muller, Philipp Eichler, Barbara D'Anna, Wen Tan, Armin Wisthaler
We report on a new method for analyzing atmospheric submicrometer particulate organic matter which combines direct particle sampling and volatilization with on-line chemical ionization mass spectrometric analysis. Technically, the method relies on the combined use of a CHARON ("Chemical Analysis of Aerosol On-line") particle inlet and a proton-transfer-reaction time-of-flight mass spectrometer (PTR-ToF-MS). Laboratory studies on target analytes showed that the ionization conditions in the PTR-ToF-MS lead to extensive fragmentation of levoglucosan and cis-pinonic acid, while protonated oleic acid and 5-cholestane molecules remain intact...
September 15, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28911222/a-ratiometric-fluorescent-probe-for-imaging-of-pantetheinase-in-living-cells
#4
Yiming Hu, Hongyu Li, Wen Shi, Huimin Ma
Pantetheinase, which catalyzes the cleavage of pantetheine to pantothenic acid (vitamin B5) and cysteamine, is involved in the regulation of oxidative stress, pantothenate recycling and cell migration. However, further elucidating the cellular function of this enzyme is largely limited by the lack of a suitable fluorescence imaging probe. By conjugating pantothenic acid with cresyl violet, herein we develop a new fluorescence probe CV-PA for the assay of pantetheinase. The probe not only possesses long analytical wavelengths but also displays linear ratiometric (I628/582 nm) fluorescence response to pantetheinase in the range of 5-400 ng/mL with a detection limit of 4...
September 15, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28861992/flow-injection-photochemical-vapor-generation-coupled-with-miniaturized-solution-cathode-glow-discharge-atomic-emission-spectrometry-for-determination-and-speciation-analysis-of-mercury
#5
Jiamei Mo, Qing Li, Xiaohong Guo, Guoxia Zhang, Zheng Wang
A novel, compact, and green method was developed for the determination and speciation analysis of mercury, based on flow injection photochemical vapor generation (PVG) coupled with miniaturized solution cathode glow discharge-atomic emission spectroscopy (SCGD-AES). The SCGD was generated between a miniature hollow titanium tube and a solution emerging from a glass capillary. Cold mercury vapor (Hg(0)) was generated by PVG and subsequently delivered to the SCGD for excitation, and finally the emission signals were recorded by a miniaturized spectrograph...
September 15, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28851222/highly-selective-sub-ppm-naked-eye-detection-of-hydrazine-with-conjugated-1-3-diketo-probes-imaging-hydrazine-in-drosophila-larvae
#6
Biswajit Roy, Sudipta Halder, Abhishek Guha, Subhajit Bandyopadhyay
A pair of pyrene- and anthracene-based turn-on fluorescent probes (1 and 2, respectively) reported here can be easily synthesized in a single-step process and also exhibit outstanding sensing behavior toward hydrazine over various competing nucleophilic species and environmentally relevant ions. The probes display dramatic enhancements in the emission intensity with as high as 83- and 173-fold increases in the presence of hydrazine. Nitrogenous bases, thiols, and lanthanides do not interfere in the fluorometric detection...
September 15, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28910098/fast-and-simple-protocols-for-mass-spectrometry-based-proteomics-of-small-fresh-frozen-uterine-tissue-sections
#7
Irena Dapic, Naomi Uwugiaren, Petra J Jansen, Garry L Corthals
Human tissues are an important link between organ specific spatial molecular information, patient pathology and patient treatment options. However, patient tissues are uniquely obtained by time and location, and limited in their availability and size. Currently little knowledge exists about appropriate and simplified protocols for routine MS-based analysis of the various types and sizes of tissues. Following standard procedures used in pathology we selected small fresh frozen uterine tissue samples to investigate how the tissue preparation protocol affected the subsequent proteomics analysis...
September 14, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28910082/macromolecular-profiling-of-organelles-in-normal-diploid-and-cancer-cells
#8
Svitlana M Levchenko, Andrey N Kuzmin, Artem Pliss, Junle Qu, Paras N Prasad
To advance an understanding of cellular regulation and function it is crucial to identify molecular contents in cellular organelles, which accommodate specific biochemical processes. Towards achievement of this goal, we applied micro-Raman-Biomolecular Component Analysis assay for molecular profiling of major organelles in live cells. We used this assay for comparative analysis of proteins 3D conformation and quantification of proteins, RNA and lipids concentrations in nucleoli, endoplasmic reticulum and mitochondria of WI-38 diploid lung fibroblasts and HeLa cancer cells...
September 14, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28868888/selective-micellar-extraction-of-ultratrace-levels-of-uranium-in-aqueous-samples-by-task-specific-ionic-liquid-followed-by-its-detection-employing-total-reflection-x-ray-fluorescence-spectrometry
#9
Abhijit Saha, Kaushik Sanyal, Neetika Rawat, Sadhan Bijoy Deb, Manoj Kumar Saxena, Bhupendra Singh Tomar
A task specific ionic liquid (TSIL) bearing phosphoramidate group, viz., N-propyl(diphenylphosphoramidate)trimethylammonium bis(trifluoromethanesulfonyl)imide, was synthesized and characterized by (1)H NMR, (13)C NMR, (31)P NMR, and IR spectroscopies, elemental (C H N S) analysis, and electrospray ionization mass spectrometry (ESI-MS). Using this TSIL a cloud point extraction (CPE) or micelle mediated extraction procedure was developed for preconcentration of uranium (U) in environmental aqueous samples. Total reflection X-ray fluorescence spectrometry was utilized to determine the concentration of U in the preconcentrated samples...
September 14, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28868887/controllable-preparation-of-cufemno4-nanospheres-as-a-novel-multifunctional-affinity-probe-for-efficient-adsorption-and-selective-enrichment-of-low-abundance-peptides-and-phosphopeptides
#10
Xing-Yu Long, Zi-Jin Zhang, Jia-Yuan Li, Dong Sheng, Hong-Zhen Lian
A facile solvothermal method for the synthesis of multifunctional magnetic CuFeMnO4 nanospheres affinity probe (NSAP) with controllable morphology and size was developed for the first time. The CuFeMnO4 nanospheres combine the brilliant features of Cu(2+), Fe(3+), and Mn(2+) ions, so their multifunction performances are embodied by strong coordination to carboxyl and amine groups of peptides (Cu(2+) and Fe(3+)), special affinity to phosphate groups of phosphopeptides (Fe(3+) and Mn(2+)), and high magnetic responsiveness in a magnetic field...
September 14, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28858525/kinetic-analysis-of-enzymes-immobilized-in-porous-film-arrays
#11
Hector D Neira, Amy E Herr
Measuring the catalytic activity of immobilized enzymes underpins development of biosensing, bioprocessing, and analytical chemistry tools. To expand the range of approaches available for measuring enzymatic activity, we report on a technique to probe activity of enzymes immobilized in porous materials in the absence of confounding mass transport artifacts. We measured reaction kinetics of calf intestinal alkaline phosphatase (CIAP) immobilized in benzophenone-modified polyacrylamide (BPMA-PAAm) gel films housed in an array of fluidically isolated chambers...
September 14, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28803479/design-of-cyclic-peptide-based-glucose-receptors-and-their-application-in-glucose-sensing
#12
Chao Li, Xin Chen, Fuyuan Zhang, Xingxing He, Guozhen Fang, Jifeng Liu, Shuo Wang
Glucose assay is of great scientific significance in clinical diagnostics and bioprocess monitoring, and to design a new glucose receptor is necessary for the development of more sensitive, selective, and robust glucose detection techniques. Herein, a series of cyclic peptide (CP) glucose receptors were designed to mimic the binding sites of glucose binding protein (GBP), and CPs' sequence contained amino acid sites Asp, Asn, His, Asp, and Arg, which constituted the first layer interactions of GBP. The properties of these CPs used as a glucose receptor or substitute for the GBP were studied by using a quartz crystal microbalance (QCM) technique...
September 14, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28903001/open-source-assisted-laboratory-automation-through-graphical-user-interfaces-and-3d-printers-application-to-equipment-hyphenation-for-higher-order-data-generation
#13
Gabriel Germán Siano, Milagros Montemurro, Mirta Raquel Alcaráz, Hector Casimiro Goicoechea
In the current analytical chemistry, even though the modeling of higher-order data can result attractive, the generation of this kind of data implies some automation challenges, which are mainly related to the hidden programming languages and electronic details of the equipment. When techniques and/or equipment hyphenation is the key to obtain higher-order data, the required simultaneous control of them demands funds for new hardware, software and licenses, and also really skilled operators. In this work we present Design of Inputs-Outputs with Sikuli (D...
September 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28902988/improvement-of-lod-in-fluorescence-detection-with-spectrally-non-uniform-background-by-optimization-of-emission-filtering
#14
Victor A Galievsky, Alexander S Stasheuski, Sergey N Krylov
The limit-of-detection (LOD) in analytical instruments with fluorescence detection can be improved by reducing noise of optical background. Efficiently reducing optical background noise in systems with spectrally non-uniform background requires complex optimization of an emission filter - the main element of spectral filtration. Here we introduce a filter-optimization method which utilizes an expression for the signal-to-noise ratio (SNR) as a function of (i) all noise components (dark, shot, and flicker), (ii) emission spectrum of the analyte, (iii) emission spectrum of the optical background, and (iv) transmittance spectrum of the emission filter...
September 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28902506/non-invasive-synchrotron-based-x-ray-raman-scattering-discriminates-carbonaceous-compounds-in-ancient-and-historical-materials
#15
Pierre Gueriau, Jean-Pascal Rueff, Sylvain Bernard, Josiane Albert Kaddissy, Sarah Goler, Christoph J Sahle, Dimosthenis Sokaras, Roy A Wogelius, Philip L Manning, Uwe Bergmann, Loïc Bertrand
Carbon compounds are ubiquitous and occur in a diversity of chemical forms in many systems including ancient and historic materials ranging from cultural heritage to paleontology. Determining their speciation cannot only provide unique information on their origin, but may also elucidate degradation processes. Synchrotron-based X-ray absorption near-edge structure (XANES) spectroscopy at the carbon K-edge (280-350 eV) is a very powerful method to probe carbon speciation. However, the short penetration depth of soft X-rays imposes stringent constraints on sample type, preparation and analytical environment...
September 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28901744/time-resolved-fluorescence-immunochromatographic-assay-developed-using-two-idiotypic-nanobodies-for-rapid-quantitative-and-simultaneous-detection-of-aflatoxin-and-zearalenone-in-maize-and-its-products
#16
Xiaoqian Tang, Peiwu Li, Qi Zhang, Zhaowei Zhang, Wen Zhang, Jun Jiang
Aflatoxins and zearalenone (ZEN) are highly common mycotoxins in maize and maize-based products. This study aimed to report a time-resolved fluorescence immunochromatographic assay (TRFICA) developed using two idiotypic nanobodies for rapid, quantitative, and simultaneous detection of aflatoxin B1 (AFB1) and ZEN in maize and its products. A novel Eu/Tb(III) nanosphere with enhanced fluorescence was prepared as a label and conjugated to anti-idiotypic nanobody (AIdnb) and monoclonal antibody (mAb). On the basis of nanosphere-antibody conjugation, two patterns of competitive time-resolved strip methods (AIdnb-TRFICA and mAb-TRFICA) were established and compared...
September 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28901741/glycoforest-1-0
#17
Oliver Horlacher, Chunsheng Jin, Davide Alocci, Julien Mariethoz, Markus Müller, Niclas G Karlsson, Frédérique Lisacek
Tandem mass spectrometry, when combined with liquid chromatography and applied to complex mixtures produces large amounts of raw data, which needs to be analysed to identify molecular structures. This technique is widely used, particularly in glycomics. Due to a lack of high throughput glycan sequencing software, glycan spectra are predominantly sequenced manually. A challenge for writing glycan-sequencing software is that there is no direct template that can be used to infer structures detectable in an organism...
September 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28901738/determination-of-the-13c-12c-carbon-isotope-ratio-in-carbonates-and-bicarbonates-by-13c-nmr-spectroscopy
#18
Concetta Pironti, Raffaele Cucciniello, Federica Camin, Agostino Tonon, Oriana Motta, Antonio Proto
This paper is the first study focused on the innovative application of 13C NMR (Nuclear Magnetic Resonance) spectroscopy to determine the bulk 13C/12C carbon isotope ratio, at natural abundance, in inorganic carbonates and bicarbonates. In the past, 13C NMR spectroscopy (irm-13C NMR) was mainly used to measure isotope ratio monitoring with the potential of conducting 13C position-specific isotope analysis of organic molecules with high precision. The reliability of the newly developed methodology for the determination of stable carbon isotope ratio was evaluated in comparison with the method chosen in the past for these measurements, i...
September 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28901129/peptide-level-interactions-between-proteins-and-small-molecule-drug-candidates-by-hdx-ms-plimstex-and-modified-suprex-the-example-of-apoe3
#19
Hanliu Wang, Don L Rempel, Daryl E Giblin, Carl Frieden, Michael L Gross
We describe a platform utilizing two methods based on hydrogen-deuterium exchange (HDX) coupled with mass spectrometry (MS) to characterize interactions between a protein and a small-molecule ligand. The model system is apolipoprotein E3 (apoE3) and a small-molecule drug candidate. We extended PLIMSTEX (protein-ligand interactions by mass spectrometry, titration, and H/D Exchange) to the regional level by incorporating enzymatic digestion to acquire binding information for peptides. In a single experiment, we not only identified putative binding sites, but also obtained affinities of 6...
September 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28901122/correlative-microscopy-combining-secondary-ion-mass-spectrometry-and-electron-microscopy-comparison-of-intensity-hue-saturation-and-laplace-pyramid-methods-for-image-fusion
#20
Florian Vollnhals, Jean-Nicolas Audinot, Tom Wirtz, Muriel Mercier-Bonin, Isabelle Fourquaux, Birgit Schroeppel, Udo Kraushaar, Varda Lev-Ram, Mark H Ellisman, Santhana Eswara
Correlative microscopy combining various imaging modalities offers powerful insights to obtain a comprehensive understanding of physical, chemical and biological phenomena. In this article, we investigate two approaches for image-fusion in the context of combining the inherently lower-resolution chemical images obtained using Secondary Ion Mass Spectrometry (SIMS) with the high-resolution ultrastructural images obtained using Electron Microscopy (EM). We evaluate the image fusion methods with three different case-studies selected to broadly represent the typical samples in life science research: (i) histology (unlabeled tissue), (ii) nanotoxicology, and (iii) metabolism (isotopically labelled tissue)...
September 13, 2017: Analytical Chemistry
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