Genomes and Genes
Summary: An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.
- González López L, Carballar Lejarazu R, Arrevillaga Boni G, Cortes Martinez L, Cázares Raga F, Trujillo Ocampo A, et al. Lys48 ubiquitination during the intraerythrocytic cycle of the rodent malaria parasite, Plasmodium chabaudi. PLoS ONE. 2017;12:e0176533 pubmed publisher..by immunofluorescent microscopy, bidimensional electrophoresis (2-DE) combined with immunoblotting and mass spectrometry. All the studied stages presented protein ubiquitination and Lys48 polyubiquitination with more abundance ..
- Zhang J, Li J, Craig T, Kumar R, Gross M. Hydrogen-Deuterium Exchange Mass Spectrometry Reveals Calcium Binding Properties and Allosteric Regulation of Downstream Regulatory Element Antagonist Modulator (DREAM). Biochemistry. 2017;56:3523-3530 pubmed publisher..Here we describe the application of hydrogen-deuterium exchange mass spectrometry (HDX-MS) and site-directed mutagenesis to investigate the Ca2+ binding properties and the ..
- Matczuk M, Legat J, Scaletti F, Messori L, Timerbaev A, Jarosz M. The fate of differently functionalized gold nanorods in human serum: A response from capillary electrophoresis-inductively coupled plasma mass spectrometry. J Chromatogr A. 2017;1499:222-225 pubmed publisher..The method is based on a hyphenation of capillary electrophoresis (CE) with inductively coupled plasma mass spectrometry (ICP-MS), which enables monitoring the speciation changes of AuNRs under physiologically compatible ..
- Asquith M, Davin S, Stauffer P, Michell C, Janowitz C, Lin P, et al. Intestinal Metabolites Are Profoundly Altered in the Context of HLA-B27 Expression and Functionally Modulate Disease in a Rat Model of Spondyloarthritis. Arthritis Rheumatol. 2017;69:1984-1995 pubmed publisher..Metabolomic profiling was performed by high-throughput gas and liquid chromatography-based mass spectrometry. HLA-B27/?2 m-transgenic rats were treated with the microbial metabolites propionate or butyrate ..
- He J, Wu Z, Wang S, Ji X, Yang C, Xu X, et al. A decision tree-based combination of ezrin-interacting proteins to estimate the prognostic risk of patients with esophageal squamous cell carcinoma. Hum Pathol. 2017;66:115-125 pubmed publisher..We used affinity purification and mass spectrometry to identify PDIA3, CNPY2, and STMN1 as potential ezrin-interacting proteins...
- Li S, Liu C, Liu C, Zhang Y. Extraction and in vitro screening of potential acetylcholinesterase inhibitors from the leaves of Panax japonicus. J Chromatogr B Analyt Technol Biomed Life Sci. 2017;1061-1062:139-145 pubmed publisherUltrafiltration liquid chromatography-mass spectrometry (UFLC-MS) is an efficient method that can be applied to rapidly screen and identify ligands for acetylcholinesterase (AChE) from the leaves of Panax japonicus...
- Zhu L, Liang Z, Yi T, Ma Y, Zhao Z, Guo B, et al. Comparison of chemical profiles between the root and aerial parts from three Bupleurum species based on a UHPLC-QTOF-MS metabolomics approach. BMC Complement Altern Med. 2017;17:305 pubmed publisher..were analyzed and compared by the ultra-high performance liquid chromatography quadrupole/time of flight-mass spectrometry (UHPLC-QTOF-MS)...
- da Silva A, Silva N, Andrade E, Gratieri T, Setzer W, Maia J, et al. Tyrosinase inhibitory activity, molecular docking studies and antioxidant potential of chemotypes of Lippia origanoides (Verbenaceae) essential oils. PLoS ONE. 2017;12:e0175598 pubmed publisher..The best docking energies were observed with thymol and (E)-nerolidol (-79.8 kcal.mol-1), which suggested H-bonding interactions with Met281 and His263 (thymol) and His259, His263 ((E)-nerolidol). ..
- Saito Shida S, Sakai T, Nemoto S, Akiyama H. Quantitative analysis of veterinary drugs in bovine muscle and milk by liquid chromatography quadrupole time-of-flight mass spectrometry. Food Addit Contam Part A Chem Anal Control Expo Risk Assess. 2017;34:1153-1161 pubmed publisher..of veterinary drugs in bovine muscle and milk using liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) was developed...
- Zhou J, Ma X, Shi M, Chen C, Sun Y, Li J, et al. Serum metabolomics analysis reveals that obvious cardioprotective effects of low dose Sini decoction against isoproterenol-induced myocardial injury in rats. Phytomedicine. 2017;31:18-31 pubmed publisher..metabolomics approach based on ultraperformance liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF-MS)...
- Wang H, Williams D, Griffin J, Saito T, Saido T, Fraser P, et al. Time-course global proteome analyses reveal an inverse correlation between A? burden and immunoglobulin M levels in the APPNL-F mouse model of Alzheimer disease. PLoS ONE. 2017;12:e0182844 pubmed publisher..pathology of the disease, and a workflow that interrogated the brain proteome of these mice by quantitative mass spectrometry at three different ages...
- Osinalde N, Aloria K, Omaetxebarria M, Kratchmarova I. Targeted mass spectrometry: An emerging powerful approach to unblock the bottleneck in phosphoproteomics. J Chromatogr B Analyt Technol Biomed Life Sci. 2017;1055-1056:29-38 pubmed publisher..During the last decade, the development of phosphoprotein/phosphopeptide enrichment strategies and mass spectrometry (MS) technology has revolutionized the field of phosphoproteomics discovering thousands of new site-specific ..
- Ye Q, Yin W, Zhang L, Xiao H, Qi Y, Liu S, et al. The value of grip test, lysophosphatidlycholines, glycerophosphocholine, ornithine, glucuronic acid decrement in assessment of nutritional and metabolic characteristics in hepatitis B cirrhosis. PLoS ONE. 2017;12:e0175165 pubmed publisher..05). Ultra-high-performance liquid chromatography data combined with mass spectrometry (UPLC-MS) showed that levels of a variety of metabolites, including lysophosphatidylcholines (LysoPCs), ..
- Ahmed M, Chin Y, Guo X, Zhao X. Microwave assisted digestion followed by ICP-MS for determination of trace metals in atmospheric and lake ecosystem. J Environ Sci (China). 2017;55:1-10 pubmed publisher..Furthermore, enrichment factor analysis indicated that anthropogenic sources such as soil dust, biomass burning and fuel combustion influenced the metal concentrations in the atmosphere. ..
- LeKieffre C, Spangenberg J, Mabilleau G, Escrig S, Meibom A, Geslin E. Surviving anoxia in marine sediments: The metabolic response of ubiquitous benthic foraminifera (Ammonia tepida). PLoS ONE. 2017;12:e0177604 pubmed publisher..Together, our results show that anoxia induced a greatly reduced rate of heterotrophic metabolism in Ammonia tepida on a time scale of less than 24 hours, these observations are consistent with a state of dormancy. ..
- Gunaga P, Lloyd J, Mummadi S, Banerjee A, Dhondi N, Hennan J, et al. Selective IKur Inhibitors for the Potential Treatment of Atrial Fibrillation: Optimization of the Phenyl Quinazoline Series Leading to Clinical Candidate 5-[5-Phenyl-4-(pyridin-2-ylmethylamino)quinazolin-2-yl]pyridine-3-sulfonamide. J Med Chem. 2017;60:3795-3803 pubmed publisher..Further optimization of 25 to mitigate pH-dependent absorption resulted in identification of the corresponding phosphoramide prodrug (29) with an improved solubility and pharmacokinetic profile. ..
- Torma A, Groves K, Biesenbruch S, Mussell C, Reid A, Ellison S, et al. A candidate liquid chromatography mass spectrometry reference method for the quantification of the cardiac marker 1-32 B-type natriuretic peptide. Clin Chem Lab Med. 2017;55:1397-1406 pubmed publisher..BNP in plasma followed by protein precipitation, solid phase extraction (SPE) and liquid chromatography (LC) mass spectrometry (MS) was then developed and validated for the quantification of BNP at clinically relevant concentrations (..
- Venugopal K, Werkmeister E, Barois N, Saliou J, Poncet A, Huot L, et al. Dual role of the Toxoplasma gondii clathrin adaptor AP1 in the sorting of rhoptry and microneme proteins and in parasite division. PLoS Pathog. 2017;13:e1006331 pubmed publisher..In addition, we unraveled an original role for TgAP1 in the regulation of parasite division. AP?1-depleted parasites undergo normal daughter cell budding and basal complex assembly but fail to segregate at the end of cytokinesis. ..
- Hong P, Phoebe A, Jones M. Study of relative response factors and mass balance in forced degradation studies with liquid chromatography/photo-diode array detector/evaporative light scattering detector/mass spectrometry system. J Chromatogr A. 2017;1512:61-70 pubmed publisher..using photodiode array detection (PDA) in combination with evaporative light scattering (ELS) detection and mass spectrometry (MS) to assess both mass balance and the relative response factors (RRFs) in the forced degradation studies ..
- Garcia Alles L, Lesniewska E, Root K, Aubry N, Pocholle N, Mendoza C, et al. Spontaneous non-canonical assembly of CcmK hexameric components from ?-carboxysome shells of cyanobacteria. PLoS ONE. 2017;12:e0185109 pubmed publisher..PCC6803. Native mass spectrometry studies confirmed that CcmK are hexamers in solution...
- Janouskova H, El Tekle G, Bellini E, Udeshi N, Rinaldi A, Ulbricht A, et al. Opposing effects of cancer-type-specific SPOP mutants on BET protein degradation and sensitivity to BET inhibitors. Nat Med. 2017;23:1046-1054 pubmed publisher..Specifically, we provide a molecular rationale for the use of BET inhibitors to treat patients with endometrial but not prostate cancer who harbor SPOP mutations. ..
- Potriquet J, Laohaviroj M, Bethony J, Mulvenna J. A modified FASP protocol for high-throughput preparation of protein samples for mass spectrometry. PLoS ONE. 2017;12:e0175967 pubmed publisher..a modified FASP protocol which improves the rate at which protein samples can be processed prior to mass spectrometry. Adapting the original FASP protocol to a 96-well format necessitates extended spin times for buffer ..
- Gerling C, Doppler T, Heyd V, Knipper C, Kuhn T, Lehmann M, et al. High-resolution isotopic evidence of specialised cattle herding in the European Neolithic. PLoS ONE. 2017;12:e0180164 pubmed publisher..Consequently, the increasing importance of cattle in the local landscape was likely to have contributed to the progress of socio-economic differentiation in early agricultural societies in Europe. ..
- Brillen A, Walotka L, Hillebrand F, MÃ¼ller L, Widera M, Theiss S, et al. Analysis of Competing HIV-1 Splice Donor Sites Uncovers a Tight Cluster of Splicing Regulatory Elements within Exon 2/2b. J Virol. 2017;91: pubmed publisher..In particular, using RNA pulldown experiments and mass spectrometry analysis, we found members of the heterogeneous nuclear ribonucleoparticle (hnRNP) A/B family binding to a ..
- Salvagno G, Danese E, Lippi G. Preanalytical variables for liquid chromatography-mass spectrometry (LC-MS) analysis of human blood specimens. Clin Biochem. 2017;50:582-586 pubmed publisherThe use of liquid chromatography-mass spectrometry (LC-MS) for both diagnostics and research purposes is rapidly growing in clinical laboratories...
- Alfaro J, Ignatchenko A, Ignatchenko V, Sinha A, Boutros P, Kislinger T. Detecting protein variants by mass spectrometry: a comprehensive study in cancer cell-lines. Genome Med. 2017;9:62 pubmed publisher..We discuss in detail the technical and computational challenges in identifying variant peptides by MS and show that uncovering these variants allows the identification of druggable mutations within important cancer genes. ..
- Wang Y, Kim H, Sparrow J. Quercetin and cyanidin-3-glucoside protect against photooxidation and photodegradation of A2E in retinal pigment epithelial cells. Exp Eye Res. 2017;160:45-55 pubmed publisher..With ultra-high performance liquid chromatography-mass spectrometry, quercetin and cyanidin-3-glucoside also inhibited the formation of photooxidized-A2E species...
- Zawatzky K, Barhate C, Regalado E, Mann B, Marshall N, Moore J, et al. Overcoming "speed limits" in high throughput chromatographic analysis. J Chromatogr A. 2017;1499:211-216 pubmed publisher..Indeed with proper hardware sampling approaches, chromatographic analysis of microplates could approach speeds of spectrophotometric plate readers while maintaining the advantage of multicomponent detection and monitoring. ..
- Ragavan M, Kirpich A, Fu X, Burgess S, McIntyre L, Merritt M. A comprehensive analysis of myocardial substrate preference emphasizes the need for a synchronized fluxomic/metabolomic research design. Am J Physiol Heart Circ Physiol. 2017;312:H1215-H1223 pubmed publisher..This observation leads to a key observation regarding mass balance in the TCA cycle; flux through a portion of the cycle can be drastically elevated without changing the O2 consumption. ..
- Rodriguez A, Gomila R, Martorell G, Costa Bauza A, Grases F. Quantification of xanthine- and uric acid-related compounds in urine using a "dilute-and-shoot" technique coupling ultra-high-performance liquid chromatography and high-resolution Orbitrap mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci. 2017;1067:53-60 pubmed publisher..dilute-and-shoot" method combining ultra-high-performance liquid chromatography and high-resolution mass spectrometry (UHPLC/HRMS) was validated for urinary determination of twelve analytes: uric acid, hypoxanthine, xanthine, ..
- Hall J, Brault A, Vincent F, Weng S, Wang H, Dumlao D, et al. Discovery of PF-06928215 as a high affinity inhibitor of cGAS enabled by a novel fluorescence polarization assay. PLoS ONE. 2017;12:e0184843 pubmed publisher..Our results demonstrate its druggability, provide a high affinity tool compound, and establish a high throughput assay for the identification of next generation cGAS inhibitors...
- Sonntag E, Milbradt J, Svrlanska A, Strojan H, Häge S, Kraut A, et al. Protein kinases responsible for the phosphorylation of the nuclear egress core complex of human cytomegalovirus. J Gen Virol. 2017;98:2569-2581 pubmed publisher..Importantly, mass spectrometry-based proteomic analyses identified five major and nine minor sites of pUL50 phosphorylation...
- Santos C, Masullo M, Cerulli A, Mari A, Estevam C, Pizza C, et al. Isolation of antioxidant phenolics from Schinopsis brasiliensis based on a preliminary LC-MS profiling. Phytochemistry. 2017;140:45-51 pubmed publisher..10-1.86 mM. None of the tested compounds, in a range of concentrations between 12.5 and 100 ?M, caused a significant reduction of the cell number. ..
- Long S, Brown K, Drewry L, Anthony B, Phan I, Sibley L. Calmodulin-like proteins localized to the conoid regulate motility and cell invasion by Toxoplasma gondii. PLoS Pathog. 2017;13:e1006379 pubmed publisher..Consistent with this hypothesis, disruption of MyoH led to degradation of CaM3, or redistribution of CaM1 and CaM2. Collectively, our findings suggest these CaMs may interact with MyoH to control motility and cell invasion. ..
- Lee S, Gardner D, Cook D. Identification of Indole Diterpenes in Ipomoea asarifolia and Ipomoea muelleri, Plants Tremorgenic to Livestock. J Agric Food Chem. 2017;65:5266-5277 pubmed publisher..mass spectometry (HPLC-HRMS) and high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) for indole diterpene composition...
- Chen L, Lu D, Wang T, Li Z, Zhao Y, Jiang Y, et al. Identification and expression analysis of starch branching enzymes involved in starch synthesis during the development of chestnut (Castanea mollissima Blume) cotyledons. PLoS ONE. 2017;12:e0177792 pubmed publisher..These results suggested that the CmSBE enzymes mainly contributed to amylopectin synthesis and influenced the amylopectin content in the developing cotyledon, which would be beneficial to chestnut germplasm selection and breeding. ..
- Yang Z, Abdellaoui H, He W, Xu J. Ortho-Nitro Effect on the Diastereoselective Control in Sulfa-Staudinger and Staudinger Cycloadditions. Molecules. 2017;22: pubmed publisher..The current research provides further insights into the diastereoselective control in sulfa-Staudinger and Staudinger cycloadditions. ..
- Appulage D, Schug K. Silica hydride based phases for small molecule separations using automated liquid chromatography-mass spectrometry method development. J Chromatogr A. 2017;1507:115-123 pubmed publisher..and selectivity behavior were investigated using liquid chromatography coupled with triple quadrupole mass spectrometry. A set of small molecules from several chemical classes of interest, and varying in their physicochemical ..
- Ganguly A, Han X, Das U, Wang L, Loi J, Sun J, et al. Hsc70 chaperone activity is required for the cytosolic slow axonal transport of synapsin. J Cell Biol. 2017;216:2059-2074 pubmed publisher..associated with synapsin using coimmunoprecipitation and multidimensional protein identification technology mass spectrometry (MS)...
- Kim J, Kim H, Sung S. Cytotoxic pterosins from Pteris multifida roots against HCT116 human colon cancer cells. Bioorg Med Chem Lett. 2017;27:3144-3147 pubmed publisher..0±1.7?M. Additionally, 1 induced the upregulation of the caspase-9 and procaspase-9 levels in Western blots and increased the annexin V/propidium iodide (PI)-positive cell population in flow cytometry. ..
- Tech K, Tikunov A, Farooq H, Morrissy A, Meidinger J, Fish T, et al. Pyruvate Kinase Inhibits Proliferation during Postnatal Cerebellar Neurogenesis and Suppresses Medulloblastoma Formation. Cancer Res. 2017;77:3217-3230 pubmed publisher..i>Cancer Res; 77(12); 3217-30. ©2017 AACR. ..
- Grössl M, Nagy K. Benefits of ion mobility for analysing monochloropropane-diol esters. Food Addit Contam Part A Chem Anal Control Expo Risk Assess. 2017;34:1131-1139 pubmed publisher..The described results suggest that the application of ion mobility in addition to LC-MS is likely to push the boundaries of contaminant analysis especially for high-throughput screening investigations. ..
- Triebl A, Trötzmüller M, Hartler J, Stojakovic T, Köfeler H. Lipidomics by ultrahigh performance liquid chromatography-high resolution mass spectrometry and its application to complex biological samples. J Chromatogr B Analyt Technol Biomed Life Sci. 2017;1053:72-80 pubmed publisher..and quantitation of lipid molecular species using reversed phase chromatography coupled to high resolution mass spectrometry was developed...
- Duval J, Colas C, Pecher V, Poujol M, Tranchant J, Lesellier E. Hyphenation of ultra high performance supercritical fluid chromatography with atmospheric pressure chemical ionisation high resolution mass spectrometry: Part 1. Study of the coupling parameters for the analysis of natural non-polar compounds. J Chromatogr A. 2017;1509:132-140 pubmed publisher..Fluid Chromatography (UHPSFC) coupled with Atmospheric Pressure Chemical Ionization - High-resolution mass spectrometry (APCI-Q-TOF-HRMS) was developed for compounds screening from oily samples...
- Konak Ü, Certel M, Şık B, Tongur T. Development of an analysis method for determination of sulfonamides and their five acetylated metabolites in baby foods by ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry (Orbitrap-MS). J Chromatogr B Analyt Technol Biomed Life Sci. 2017;1057:81-91 pubmed publisher..5 to 96.6% with RSD?10.1%) than QuEChERS (recovery ranged from 60.9 to 85.9% with RSD?19.1%). This method was applied to the analysis of 47 different baby foods and no positive samples were found. ..
- Xie P, Xin Q, Yang S, He T, Huang Y, Zeng G, et al. Skeleton labeled 13C-carbon nanoparticles for the imaging and quantification in tumor drainage lymph nodes. Int J Nanomedicine. 2017;12:4891-4899 pubmed publisher..Therefore, the 13C-CNPs provided quantitative approach to image and quantify CNSI in biological systems. The implication in biomedical applications and biosafety evaluations of CNSI is discussed. ..
- Chen Y, Tu Z, Wang H, Zhang Q, Zhang L, Sha X, et al. The Reduction in the IgE-Binding Ability of ?-Lactoglobulin by Dynamic High-Pressure Microfluidization Coupled with Glycation Treatment Revealed by High-Resolution Mass Spectrometry. J Agric Food Chem. 2017;65:6179-6187 pubmed publisher..subjected to DHPM and glycation treatment was investigated in relation to IgE-binding ability by orbitrap mass spectrometry. After DHPM pretreatment, lower IgE-binding ability of glycated ?-LG was observed with increasing pressures...
- Candiani G, Fasoli E. A Stepwise Approach for the Isolation and the Identification of Chemically Reactive Exofacial Protein Thiols. Protein Pept Lett. 2017;24:633-642 pubmed publisher..We devised an enabling methodology to selectively pick up, recover and characterize chemically reactive EPTs. ..
- Castro G, Rodriguez I, Ramil M, Cela R. Evaluation of nitrate effects in the aqueous photodegradability of selected phenolic pollutants. Chemosphere. 2017;185:127-136 pubmed publisher..of transformation products (TPs) were investigated by liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF-MS). Nitrate showed a positive effect in the removal of selected pollutants...
- Aghera N, Udgaonkar J. Stepwise Assembly of ?-Sheet Structure during the Folding of an SH3 Domain Revealed by a Pulsed Hydrogen Exchange Mass Spectrometry Study. Biochemistry. 2017;56:3754-3769 pubmed publisher..study, the folding of the SH3 domain of PI3 kinase has been characterized using pulsed hydrogen exchange mass spectrometry (HX-MS)...
- Sai Saraswathi V, Saravanan D, Santhakumar K. Isolation of quercetin from the methanolic extract of Lagerstroemia speciosa by HPLC technique, its cytotoxicity against MCF-7 cells and photocatalytic activity. J Photochem Photobiol B. 2017;171:20-26 pubmed publisher..speciosa. Hence we expect that this can be used to treat the waste water in near future based on the photocatalytic technique. ..
- Carabetta V, Cristea I. Regulation, Function, and Detection of Protein Acetylation in Bacteria. J Bacteriol. 2017;199: pubmed publisher..Advancements in mass spectrometry-based proteomics have led to the discovery that bacteria contain hundreds of acetylated proteins, contrary ..