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https://www.readbyqxmd.com/read/27922621/sharing-brain-mapping-statistical-results-with-the-neuroimaging-data-model
#1
Camille Maumet, Tibor Auer, Alexander Bowring, Gang Chen, Samir Das, Guillaume Flandin, Satrajit Ghosh, Tristan Glatard, Krzysztof J Gorgolewski, Karl G Helmer, Mark Jenkinson, David B Keator, B Nolan Nichols, Jean-Baptiste Poline, Richard Reynolds, Vanessa Sochat, Jessica Turner, Thomas E Nichols
Only a tiny fraction of the data and metadata produced by an fMRI study is finally conveyed to the community. This lack of transparency not only hinders the reproducibility of neuroimaging results but also impairs future meta-analyses. In this work we introduce NIDM-Results, a format specification providing a machine-readable description of neuroimaging statistical results along with key image data summarising the experiment. NIDM-Results provides a unified representation of mass univariate analyses including a level of detail consistent with available best practices...
December 6, 2016: Scientific Data
https://www.readbyqxmd.com/read/27862147/signal-preprocessing-multivariate-analysis-and-software-tools-for-ma-ldi-tof-mass-spectrometry-imaging-for-biological-applications
#2
REVIEW
Pere Ràfols, Dídac Vilalta, Jesús Brezmes, Nicolau Cañellas, Esteban Del Castillo, Oscar Yanes, Noelia Ramírez, Xavier Correig
Mass spectrometry imaging (MSI) is a label-free analytical technique capable of molecularly characterizing biological samples, including tissues and cell lines. The constant development of analytical instrumentation and strategies over the previous decade makes MSI a key tool in clinical research. Nevertheless, most MSI studies are limited to targeted analysis or the mere visualization of a few molecular species (proteins, peptides, metabolites, or lipids) in a region of interest without fully exploiting the possibilities inherent in the MSI technique, such as tissue classification and segmentation or the identification of relevant biomarkers from an untargeted approach...
November 9, 2016: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27859457/time-of-flight-mass-spectrometry-introduction-to-the-basics
#3
REVIEW
Ulrich Boesl
The intention of this tutorial is to introduce into the basic concepts of time-of-flight mass spectrometry, beginning with the most simple single-stage ion source with linear field-free drift region and continuing with two-stage ion sources combined with field-free drift regions and ion reflectors-the so-called reflectrons. Basic formulas are presented and discussed with the focus on understanding the physical relations of geometric and electric parameters, initial distribution of ionic parameters, ion flight times, and ion flight time incertitude...
January 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27780848/sucrose-non-fermenting-related-kinase-enzyme-mediated-rho-associated-kinase-signaling-is-responsible-for-cardiac-function
#4
Stephanie M Cossette, Vijesh J Bhute, Xiaoping Bao, Leanne M Harmann, Mark A Horswill, Indranil Sinha, Adam Gastonguay, Shabnam Pooya, Michelle Bordas, Suresh N Kumar, Shama P Mirza, Sean Palecek, Jennifer Strande, Ramani Ramchandran
BACKGROUND: -Cardiac metabolism is critical for the functioning of the heart, and disturbance in this homeostasis is likely to influence cardiac disorders or cardiomyopathy. Our lab has previously shown that sucrose non-fermenting related kinase (SNRK) enzyme, which belongs to the AMP-activated kinase (AMPK) family, was essential for cardiac metabolism in mammals. Snrk global homozygous knockout (KO) mice die at postnatal day 0, and conditional deletion of Snrk in cardiomyocytes (Snrk cmcKO) leads to cardiac failure, and death by 8-10 months...
October 25, 2016: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/27750373/mass-spectrometric-strategies-for-the-investigation-of-biomarkers-of-illicit-drug-use-in-wastewater
#5
Félix Hernández, Sara Castiglioni, Adrian Covaci, Pim de Voogt, Erik Emke, Barbara Kasprzyk-Hordern, Christoph Ort, Malcolm Reid, Juan V Sancho, Kevin V Thomas, Alexander L N van Nuijs, Ettore Zuccato, Lubertus Bijlsma
The analysis of illicit drugs in urban wastewater is the basis of wastewater-based epidemiology (WBE), and has received much scientific attention because the concentrations measured can be used as a new non-intrusive tool to provide evidence-based and real-time estimates of community-wide drug consumption. Moreover, WBE allows monitoring patterns and spatial and temporal trends of drug use. Although information and expertise from other disciplines is required to refine and effectively apply WBE, analytical chemistry is the fundamental driver in this field...
October 17, 2016: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27741559/the-arc-of-mass-spectrometry-exchange-formats-is-long-but-it-bends-toward-hdf5
#6
Manor Askenazi, Hisham Ben Hamidane, Johannes Graumann
The evolution of data exchange in Mass Spectrometry spans decades and has ranged from human-readable text files representing individual scans or collections thereof (McDonald et al., 2004) through the official standard XML-based (Harold, Means, & Udemadu, 2005) data interchange standard (Deutsch, 2012), to increasingly compressed (Teleman et al., 2014) variants of this standard sometimes requiring purely binary adjunct files (Römpp et al., 2011). While the desire to maintain even partial human readability is understandable, the inherent mismatch between XML's textual and irregular format relative to the numeric and highly regular nature of actual spectral data, along with the explosive growth in dataset scales and the resulting need for efficient (binary and indexed) access has led to a phenomenon referred to as "technical drift" (Davis, 2013)...
October 14, 2016: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27611504/marine-environment-pollution-the-contribution-of-mass-spectrometry-to-the-study-of-seawater
#7
Emanuele Magi, Marina Di Carro
The study of marine pollution has been traditionally addressed to persistent chemicals, generally known as priority pollutants; a current trend in environmental analysis is a shift toward "emerging pollutants," defined as newly identified or previously unrecognized contaminants. The present review is focused on the peculiar contribution of mass spectrometry (MS) to the study of pollutants in the seawater compartment. The work is organized in five paragraphs where the most relevant groups of pollutants, both "classical" and "emerging," are presented and discussed, highlighting the relative data obtained by the means of different MS techniques...
September 9, 2016: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27602546/computational-methods-and-challenges-in-hydrogen-deuterium-exchange-mass-spectrometry
#8
Jürgen Claesen, Tomasz Burzykowski
Hydrogen/Deuterium exchange (HDX) has been applied, since the 1930s, as an analytical tool to study the structure and dynamics of (small) biomolecules. The popularity of using HDX to study proteins increased drastically in the last two decades due to the successful combination with mass spectrometry (MS). Together with this growth in popularity, several technological advances have been made, such as improved quenching and fragmentation. As a consequence of these experimental improvements and the increased use of protein-HDXMS, large amounts of complex data are generated, which require appropriate analysis...
September 7, 2016: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27593344/precise-analysis-of-gallium-isotopic-composition-by-mc-icp-ms
#9
Wei Yuan, Jiu Bin Chen, Jean-Louis Birck, Zuo Ying Yin, Sheng Liu Yuan, Hong Ming Cai, Zhong Wei Wang, Qiang Huang, Zhu Hong Wang
Though an isotope approach could be beneficial for better understanding the biogeochemical cycle of gallium (Ga), an analogue of the monoisotopic element aluminum (Al), the geochemistry of Ga isotopes has not been widely elaborated. We developed a two-step method for purifying Ga from geological (biological) samples for precise measurement of Ga isotope ratio using multicollector inductively coupled plasma mass spectrometry (MC-ICP-MS). Ga was thoroughly separated from other matrix elements using two chromatographic columns loaded with AG 1-X4 and Ln-spec resin, respectively...
October 4, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27580014/mass-spectral-fragmentation-of-trimethylsilylated-small-molecules
#10
Zijuan Lai, Oliver Fiehn
Mass spectrometry-based untargeted metabolomics detects many peaks that cannot be identified. While advances have been made for automatic structure annotations in LC-electrospray-MS/MS, no open source solutions are available for hard electron ionization used in GC-MS. In metabolomics, most compounds bear moieties with acidic protons, for example, amino, hydroxyl, or carboxyl groups. Such functional groups increase the boiling points of metabolites too much for use in GC-MS. Hence, in GC-MS-focused metabolomics, derivatization of these groups is essential and has been employed since the 1960s...
August 31, 2016: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27579891/mass-spectrometry-derived-systems-biology-technologies-delineate-the-system-s-biochemical-applications-of-siderophores
#11
Qiao Su, Guang Xu, Tianbing Guan, Yumei Que, Haitao Lu
Siderophores are chemically diverse secondary metabolites that primarily assist the host organisms to chelate iron. Siderophores are biosynthesized by many biological organisms, including bacteria, fungi, and plants and they are responsible for a variety of biological functions beyond capture iron. Thus, they could provide a novel understanding of host-pathogen interactions, plant physiology, disease pathogenesis, and drug development. However, knowledge gaps in analytical technologies, chemistry, and biology have severely impeded the applications of siderophores, and a new strategy is urgently needed to bridge these gaps...
August 31, 2016: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27498756/anion-redox-chemistry-in-the-cobalt-free-3d-transition-metal-oxide-intercalation-electrode-li-li0-2ni0-2mn0-6-o2
#12
Kun Luo, Matthew R Roberts, Niccoló Guerrini, Nuria Tapia-Ruiz, Rong Hao, Felix Massel, David M Pickup, Silvia Ramos, Yi-Sheng Liu, Jinghua Guo, Alan V Chadwick, Laurent C Duda, Peter G Bruce
Conventional intercalation cathodes for lithium batteries store charge in redox reactions associated with the transition metal cations, e.g., Mn(3+/4+) in LiMn2O4, and this limits the energy storage of Li-ion batteries. Compounds such as Li[Li0.2Ni0.2Mn0.6]O2 exhibit a capacity to store charge in excess of the transition metal redox reactions. The additional capacity occurs at and above 4.5 V versus Li(+)/Li. The capacity at 4.5 V is dominated by oxidation of the O(2-) anions accounting for ∼0.43 e(-)/formula unit, with an additional 0...
September 7, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27463413/controlled-formation-of-heteroleptic-pd2-la-2-lb-2-4-cages
#13
Dan Preston, Jonathan E Barnsley, Keith C Gordon, James D Crowley
Metallosupramolecular architectures are beginning to be exploited for a range of applications including drug delivery, catalysis, molecular recognition, and sensing. For the most part these achievements have been made with high-symmetry metallosupramolecular architectures composed of just one type of ligand and metal ion. Recently, considerable efforts have been made to generate metallosupramolecular architectures that are made up of multiple different ligands and/or metals ions in order to obtain more complex systems with new properties...
August 24, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27454229/orthogonal-synthesis-of-easy-to-read-information-containing-polymers-using-phosphoramidite-and-radical-coupling-steps
#14
Gianni Cavallo, Abdelaziz Al Ouahabi, Laurence Oswald, Laurence Charles, Jean-François Lutz
A new orthogonal solid-phase iterative strategy is proposed for the synthesis of sequence-coded polymers. This approach relies on the use of two successive chemoselective steps: (i) phosphoramidite coupling, and (ii) radical-radical coupling. These repeated steps can be performed using two different types of building blocks, i.e. a phosphoramidite monomer that also contains an alkyl bromide and a hydroxy-functionalized nitroxide. The phosphoramidite and the hydroxy group are reacted in step (i), thus leading to a phosphite that is oxidized in situ into a phosphate bond...
August 3, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27423866/exploring-the-dynamic-relationship-between-cellular-metabolism-and-chromatin-structure-using-silac-mass-spec-and-chip-sequencing
#15
P Mews, S L Berger
Metabolic state and chromatin structure are tightly linked, enabling adaptation of gene expression to changing environment and metabolism. The bioenergetic pathways and enzymes that provide metabolic cofactors for histone modification have recently emerged as central regulators of chromatin. Current research therefore focuses on the dynamic interface of cellular metabolism and chromatin structure. Here, we provide an adaptable approach to examine broadly in changing physiological states, how chromatin structure is dynamically modulated by metabolic activity...
2016: Methods in Enzymology
https://www.readbyqxmd.com/read/27420733/the-quest-for-improved-reproducibility-in-maldi-mass-spectrometry
#16
Matthew B O'Rourke, Steven P Djordjevic, Matthew P Padula
Reproducibility has been one of the biggest hurdles faced when attempting to develop quantitative protocols for MALDI mass spectrometry. The heterogeneous nature of sample recrystallization has made automated sample acquisition somewhat "hit and miss" with manual intervention needed to ensure that all sample spots have been analyzed. In this review, we explore the last 30 years of literature and anecdotal evidence that has attempted to address and improve reproducibility in MALDI MS. Though many methods have been attempted, we have discovered a significant publication history surrounding the use of nitrocellulose as a substrate to improve homogeneity of crystal formation and therefore reproducibility...
July 15, 2016: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27412762/high-sensitivity-crosslink-detection-coupled-with-integrative-structure-modeling-in-the-mass-spec-studio
#17
Vladimir Sarpe, Atefeh Rafiei, Morgan Hepburn, Nicholas Ostan, Anthony B Schryvers, David C Schriemer
The Mass Spec Studio package was designed to support the extraction of hydrogen-deuterium exchange and covalent labeling data for a range of mass spectrometry (MS)-based workflows, to integrate with restraint-driven protein modeling activities. In this report, we present an extension of the underlying Studio framework and provide a plug-in for crosslink (XL) detection. To accommodate flexibility in XL methods and applications, while maintaining efficient data processing, the plug-in employs a peptide library reduction strategy via a presearch of the tandem-MS data...
September 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27403762/mass-spectrometric-epitope-mapping
#18
Kwabena F M Opuni, Mahmoud Al-Majdoub, Yelena Yefremova, Reham F El-Kased, Cornelia Koy, Michael O Glocker
Mass spectrometric epitope mapping has become a versatile method to precisely determine a soluble antigen's partial structure that directly interacts with an antibody in solution. Typical lengths of investigated antigens have increased up to several 100 amino acids while experimentally determined epitope peptides have decreased in length to on average 10-15 amino acids. Since the early 1990s more and more sophisticated methods have been developed and have forwarded a bouquet of suitable approaches for epitope mapping with immobilized, temporarily immobilized, and free-floating antibodies...
July 12, 2016: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27403644/tandem-mass-spectral-libraries-of-peptides-and-their-roles-in-proteomics-research
#19
Wenguang Shao, Henry Lam
Proteomics is a rapidly maturing field aimed at the high-throughput identification and quantification of all proteins in a biological system. The cornerstone of proteomic technology is tandem mass spectrometry of peptides resulting from the digestion of protein mixtures. The fragmentation pattern of each peptide ion is captured in its tandem mass spectrum, which enables its identification and acts as a fingerprint for the peptide. Spectral libraries are simply searchable collections of these fingerprints, which have taken on an increasingly prominent role in proteomic data analysis...
July 12, 2016: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/27341181/recent-2000-2015-developments-in-the-analysis-of-minor-unknown-natural-products-based-on-characteristic-fragment-information-using-lc-ms
#20
Tian Cai, Ze-Qin Guo, Xiao-Ying Xu, Zhi-Jun Wu
Liquid chromatography-Mass Spectrometry (LC-MS) has been widely used in natural product analysis. Global detection and identification of nontargeted components are desirable in natural product research, for example, in quality control of Chinese herbal medicine. Nontargeted components analysis continues to expand to exciting life science application domains such as metabonomics. With this background, the present review summarizes recent developments in the analysis of minor unknown natural products using LC-MS and mainly focuses on the determination of the molecular formulae, selection of precursor ions, and characteristic fragmentation patterns of the known compounds...
June 24, 2016: Mass Spectrometry Reviews
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