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Alexander Hogrebe, Louise von Stechow, Dorte B Bekker-Jensen, Brian T Weinert, Christian D Kelstrup, Jesper V Olsen
Comprehensive mass spectrometry (MS)-based proteomics is now feasible, but reproducible quantification remains challenging, especially for post-translational modifications such as phosphorylation. Here, we compare the most popular quantification techniques for global phosphoproteomics: label-free quantification (LFQ), stable isotope labeling by amino acids in cell culture (SILAC) and MS2 - and MS3 -measured tandem mass tags (TMT). In a mixed species comparison with fixed phosphopeptide ratios, we find LFQ and SILAC to be the most accurate techniques...
March 13, 2018: Nature Communications
Julia Sommer, Susanne Fister, Tobias Gundolf, Birgit Bromberger, Patrick-Julian Mester, Anna Kristina Witte, Roland Kalb, Peter Rossmanith
For three decades now, ionic liquids (ILs), organic salts comprising only ions, have emerged as a new class of pharmaceuticals. Although recognition of the antimicrobial effects of ILs is growing rapidly, there is almost nothing known about their possible virucidal activities. This probably reflects the paucity of understanding virus inactivation. In this study, we performed a systematic analysis to determine the effect of specific structural motifs of ILs on three different biological test systems (viruses, bacteria and enzymes)...
March 9, 2018: International Journal of Molecular Sciences
Matthew Sonnett, Eyan Yeung, Martin Wühr
Quantitative analysis of proteomes across multiple time points, organelles, and perturbations is essential for understanding both fundamental biology and disease states. The development of isobaric tags (e.g. TMT) have enabled the simultaneous measurement of peptide abundances across several different conditions. These multiplexed approaches are promising in principle because of advantages in throughput and measurement quality. However, in practice existing multiplexing approaches suffer from key limitations...
March 9, 2018: Analytical Chemistry
David O De Haan, Enrico Tapavicza, Matthieu Riva, Tianqu Cui, Jason Douglas Surratt, Adam C Smith, Mary-Caitlin Jordan, Shiva Nilakantan, Marisol Almodovar, Tiffany N Stewart, Alexia de Loera, Audrey C De Haan, Mathieu Cazaunau, Aline Gratien, Edouard Pangui, Jean-Francois Doussin
Aqueous methylglyoxal chemistry has often been implicated as an important source of oligomers in atmospheric aerosol. Here we report on chemical analysis of brown carbon aerosol particles collected from cloud cycling / photolysis chamber experiments, where gaseous methylglyoxal and methylamine interacted with glycine, ammonium or methylammonium sulfate seed particles. Eighteen N-containing oligomers were identified in the particulate phase by liquid chromatography / diode array detection / electrospray ionization high-resolution quadrupole time-of-flight mass spectrometry...
March 6, 2018: Environmental Science & Technology
Rachael E Wilson, Andrea Jaquins-Gerstl, Stephen G Weber
We have developed a method for online collection and quantitation of neuropeptides in rat brain microdialysates using on-column dimethylation with capillary liquid chromatography - tandem mass spectrometry (cLC - MS2). This method addresses a number of the challenges of quantifying neuropeptides with cLC - MS. It is also a completely automated and robust method for the preparation of stable isotope labeled - peptide internal standards to correct for matrix effects and thus ensure accurate quantitation. Originally developed for tissue-derived proteomics samples (Raijmakers, et al...
March 5, 2018: Analytical Chemistry
Xiaoli Fan, Yurong An, Zhifen Luo, Yan Hu, Baihai Li, Woon-Ming Lau
Stable nano-triangles of monolayer transitional metal dichalcogenides (referred therein as MS2 mNTs) grown via ordinary deposition conditions, when M=Mo or W, exhibit a peculiar 3-foldperiodic size-dependence in electronic and chemical properties. For "k" being the number of M atoms per edge, mNTs are: (a) intrinsic-semiconducting when k=3i+1, such as k=7,10,13,16; (b) metallic-like with no bandgap when k=3i; (c) n+ semiconducting when k=3i-1. Besides changes in electronic properties, the catalytic properties for hydrogen evolution reaction also switch from active for k=3i and 3i-1 to inactive for k=3i+1...
March 5, 2018: Journal of Physical Chemistry Letters
Mustapha Tacherfiout, Petar D Petrov, Marco Mattonai, Erika Ribechini, Joan Ribot, M Luisa Bonet, Bachra Khettal
The Mediterranean buckthorn, Rhamnus alaternus L., is a plant used in traditional medicine in Mediterranean countries. We aimed at characterizing its phenolic compounds and explore potential antihyperlipidemic activity of this plant. The profile of phenolic compounds in R. alaternus leaf crude methanolic extract (CME) and its liquid-liquid extraction-derived fractions were analyzed by high-performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC/ESI-MS2 ). Effects of CME on: circulating lipids in rats with Triton WR-1339-induced hyperlipidemia, intracellular lipid accumulation and expression of genes of fatty acid metabolism in human hepatoma HepG2 cells, and adipogenesis in the 3T3-L1 murine adipocyte cell model were assessed...
March 1, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
B Tian, H F Li, H Yang, D L Song, X W Bai, Y L Zhao
In this paper, a SOI (silicon-on-insulator)-based piezoresistive fluid flow sensor is presented; the presented flow sensor mainly consists of a nylon sensing head, stainless steel cantilever beam, SOI sensor chip, printed circuit board, half-cylinder gasket, and stainless steel shell. The working principle of the sensor and some detailed contrastive analysis about the sensor structure were introduced since the nylon sensing head and stainless steel cantilever beam have distinct influence on the sensor performance; the structure of nylon sensing head and stainless steel cantilever beam is also discussed...
February 2018: Review of Scientific Instruments
Haihong Zha, Yuping Cai, Yandong Yin, Zhuozhong Wang, Kang Li, Zheng-Jiang Zhu
The complexity of metabolome presents a great analytical challenge for quantitative metabolite profiling, and restricts the application of metabolomics in biomarker discovery. Targeted metabolomics using multiple-reaction monitoring (MRM) technique has excellent capability for quantitative analysis, but suffers from the limited metabolite coverage. To address this challenge, we developed a new strategy, namely, SWATHtoMRM, which utilizes the broad coverage of SWATH-MS technology to develop high-coverage targeted metabolomics method...
February 27, 2018: Analytical Chemistry
Marta Robledo, Ana M Matia-González, Natalia I García-Tomsig, José I Jiménez-Zurdo
The identification of the protein partners of bacterial small noncoding RNAs (sRNAs) is essential to understand the mechanistic principles and functions of riboregulation in prokaryotic cells. Here, we describe an optimized affinity chromatography protocol that enables purification of in vivo formed sRNA-protein complexes in Sinorhizobium meliloti, a genetically tractable nitrogen-fixing plant symbiotic bacterium. The procedure requires the tagging of the desired sRNA with the MS2 aptamer, which is affinity-captured by the MS2-MBP protein conjugated to an amylose resin...
2018: Methods in Molecular Biology
Marie-Claude Carrier, Guillaume Laliberté, Eric Massé
Small regulatory RNAs (sRNAs) are ubiquitous regulatory molecules expressed in living cells. In prokaryotes, sRNAs usually bind to target mRNAs to either promote their degradation or interfere with translation initiation. Because a single sRNA can regulate a considerable number of target mRNAs, we seek to identify those targets rapidly and reliably. Here, we present a robust method based on the co-purification of target mRNAs bound to MS2-tagged sRNAs expressed in vivo. After purification of the tagged-sRNA, we use RNAseq to determine the identity of all RNA interacting partners and their enrichment level...
2018: Methods in Molecular Biology
Corryn E Chini, Gregory L Fisher, Ben Johnson, Michael M Tamkun, Mary L Kraft
Advances in three-dimensional secondary ion mass spectrometry (SIMS) imaging have enabled visualizing the subcellular distributions of various lipid species within individual cells. However, the difficulty of locating organelles using SIMS limits efforts to study their lipid compositions. Here, the authors have assessed whether endoplasmic reticulum (ER)-Tracker Blue White DPX® , which is a commercially available stain for visualizing the endoplasmic reticulum using fluorescence microscopy, produces distinctive ions that can be used to locate the endoplasmic reticulum using SIMS...
February 26, 2018: Biointerphases
Michael Versoza, Wonseok Jung, Mona Loraine Barabad, Yongil Lee, Kyomin Choi, Duckshin Park
The inactivation of viruses that retain their infectivity when transmitted through the air is challenging. To address this issue, this study used a non-contact ultrasound transducer (NCUT) to generate shock waves in the air at specific distances, input voltages, and exposure durations, targeting bacteriophage virus aerosols captured on to H14 HEPA filters. Initially, a frequency of 27.56 kHz (50V) at 25-mm distance was used, which yielded an inactivation efficiency of up to 32.69 ± 12.10%. Other frequencies at shorter distances were investigated, where 29...
February 20, 2018: Journal of Virological Methods
Suntae Lee, Shota Tasaki, Akihiko Hata, Naoyuki Yamashita, Hiroaki Tanaka
Evaluating the reduction of virus load in water reclamation plants is important to ensuring the hygienic safety of the reclaimed water. A virus-spiking test is usually used to estimate virus reduction but is not practicable at large-scale plants. Thus, we evaluated virus reduction by ultrafiltration (UF) plus ultraviolet (UV) irradiation at a large-scale reclamation plant (1000 m3 /d) by quantifying indigenous F-specific RNA bacteriophages (FRNAPHs). To detect the infectious FRNAPH, we used both plaque assay and integrated culture-reverse-transcription polymerase chain reaction combined with the most probable number assay, which can detect infectious FRNAPH genotypes...
February 23, 2018: Environmental Technology
Lisa M Casanova, Kimberly Erukunuakpor, Colleen S Kraft, Joel M Mumma, Francis T Durso, Ashley N Ferguson, Christina L Gipson, Victoria L Walsh, Craig Zimring, Jennifer DuBose, Jesse T Jacob
Background: Personal protective equipment (PPE) protects healthcare workers (HCWs) caring for patients with Ebola virus disease (EVD), and PPE doffing is a critical point for preventing viral self-contamination. We assessed contamination of skin, gloves, and scrubs after doffing Ebola-level PPE contaminated with surrogate viruses: bacteriophages MS2 and Φ6. Methods: In a medical biocontainment unit, HCWs (n = 10) experienced in EVD care donned and doffed PPE following unit protocols that incorporate trained observer guidance and alcohol-based hand rub (ABHR)...
February 17, 2018: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
Joel M Mumma, Francis T Durso, Ashley N Ferguson, Christina L Gipson, Lisa Casanova, Kimberly Erukunuakpor, Colleen S Kraft, Victoria L Walsh, Craig Zimring, Jennifer DuBose, Jesse T Jacob
Background: Doffing protocols for personal protective equipment (PPE) are critical for keeping healthcare workers (HCWs) safe during care of patients with Ebola virus disease. We assessed the relationship between errors and self-contamination during doffing. Methods: Eleven HCWs experienced with doffing Ebola-level PPE participated in simulations in which HCWs donned PPE marked with surrogate viruses (ɸ6 and MS2), completed a clinical task, and were assessed for contamination after doffing...
February 17, 2018: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
Xiaoyan Guan, Le Zhang, Jette Wypych
Disulfide linkage is critical to protein folding and structural stability. The location of disulfide linkages for antibodies is routinely discovered by comparing the chromatograms of the reduced and non-reduced peptide mapping with location identification confirmed by collision-induced dissociation (CID) mass spectrometry (MS)/MS. However, CID product spectra of disulfide-linked peptides can be difficult to interpret, and provide limited information on the backbone region within the disulfide loop. Here, we applied an electron-transfer dissociation (ETD)/CID combined fragmentation method that identifies the disulfide linkage without intensive LC comparison, and yet maps the disulfide location accurately...
February 22, 2018: MAbs
Simon Meister, Matthew E Verbyla, Marius Klinger, Tamar Kohn
The susceptibility of waterborne viruses to disinfection is known to vary between viruses and even between closely related strains, yet the extent of this variation is not known. Here, different enteroviruses (six strains of coxsackievirus B5, two strains of coxsackievirus B4 and one strain of coxackievirus B1) were isolated from wastewater and inactivated by UV254 , sunlight, free chlorine (FC), chlorine dioxide (ClO2 ), and heat. Inactivation kinetics of these isolates were compared with those of laboratory enterovirus strains (CVB5 Faulkner and echovirus 11 Gregory) and MS2 bacteriophage...
February 21, 2018: Environmental Science & Technology
Matthew J Berberich, Joao A Paulo, Robert A Everley
Protein phosphorylation is critically important for many cellular processes, including progression through the cell cycle, cellular metabolism and differentiation. The addition of isobaric labeling, e.g., Tandem Mass Tags (TMT), to phosphoproteomics workflows enables both relative and absolute quantitation of these phosphorylation events. Traditional TMT workflows identify peptides using fragment ions at the MS2 level and quantify reporter ions at the MS3 level. However, in addition to the TMT reporter ions, MS3 spectra also include fragment ions which can be used to identify peptides...
February 20, 2018: Journal of Proteome Research
Zoltan Szabo, James R Thayer, Dietmar Reusch, Yury Agroskin, Rosa Viner, Jeff Rohrer, Sachin P Patil, Michael Krawitzky, Andreas Huhmer, Nebojsa Avdalovic, Shaheer H Khan, Yan Liu, Christopher Pohl
Comprehensive characterization of the N-glycome of a therapeutic is challenging because glycans may harbor numerous modifications (e.g. phosphorylation, sulfation, sialic acids with possible O-acetylation). The current report presents a comparison of two chromatographic platforms for the comprehensive characterization of a recombinant human erythropoietin (rhEPO) N-glycome. The two platforms include a common workflow based on 2-AB-derivatization and hydrophilic interaction chromatography (HILIC) and a native N-linked glycan workflow employing high performance anion exchange (HPAE) chromatography...
February 16, 2018: Journal of Proteome Research
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