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Scanning A uger spectromicroscopy using the S cope F oundry software platform

Published: Mar 9, 2018

Author(s): Daniel B. Durham, D. Frank Ogletree, Edward S. Barnard

Journal: Surface and Interface Analysis

We have developed an open‐source, Python‐based software platform called ScopeFoundry for performing complex, multidimensional microscopy experiments that integrate diverse types of experimental hardware. ScopeFoundry streamlines experiment development by providing a modular environment where hardware controls and measurement schemes can be arranged and customized. Important software tasks such as data management and user interface...

Read More thumbnail image: Scanning A uger spectromicroscopy using the S cope F oundry software platform

Uptake and metabolism of the antidepressants sertraline, clomipramine, and trazodone in a garden cress ( Lepidium sativum ) model

Published: Mar 8, 2018

Author(s): Bernd Reichl, Markus Himmelsbach, Lisa Emhofer, Christian W. Klampfl, Wolfgang Buchberger

Journal: ELECTROPHORESIS

Abstract Environmental contamination with pharmaceuticals has received growing attention in recent years. Several studies describe the presence of traces of drugs in water bodies and soils and their impacts on nontarget organisms including plants. Due to these facts investigations of the uptake and metabolism of pharmaceuticals in organisms is an emerging research area. The present study demonstrates the analysis of three selected...

Read More thumbnail image: Uptake and metabolism of the antidepressants sertraline clomipramine and trazodone in a garden cress  Lepidium sativum  model

Investigating capillary electrophoresis‐mass spectrometry for the analysis of common post‐translational modifications

Published: Mar 8, 2018

Author(s): Klaus Faserl, Bettina Sarg, Peter Gruber, Herbert H. Lindner

Journal: ELECTROPHORESIS

Abstract Capillary electrophoresis coupled to mass spectrometry is a very efficient analytical method for the analysis of post‐translational modifications because of its high separation efficiency and high detection sensitivity. Here we applied CE‐MS using three differently coated separation capillaries for in‐depth analysis of a set of 70 synthetic post‐translationally modified peptides (including phosphorylation, acetylation,...

Read More thumbnail image: Investigating capillary electrophoresismass spectrometry for the analysis of common posttranslational modifications

Enhancement of the conductivity detection signal in capillary electrophoresis systems using neutral cyclodextrins as sweeping agents

Published: Mar 8, 2018

Author(s): Milan Boublík, Martina Riesová, Pavel Dubský, Bohuslav Gaš

Journal: ELECTROPHORESIS

Abstract Conductivity detection is a universal detection technique often encountered in electrophoretic separation systems, especially in modern chip‐electrophoresis based devices. On the other hand, it is sparsely combined with another contemporary trend of enhancing limits of detection by means of various preconcentration strategies. This can be attributed to the fact that a preconcentration experimental setup usually brings about...

Read More thumbnail image: Enhancement of the conductivity detection signal in capillary electrophoresis systems using neutral cyclodextrins as sweeping agents

Simultaneous construction of dual Borgen plots. II: Algorithmic enhancement for applications to noisy spectral data

Published: Mar 8, 2018

Author(s): Mathias Sawall, Annekathrin Moog, Christoph Kubis, Henning Schröder, Detlef Selent, Robert Franke, Alexander Brächer, Armin Börner, Klaus Neymeyr

Journal: Journal of Chemometrics

Abstract Borgen plots are low‐dimensional representations of the set of all nonnegative factorizations of spectral data matrices. Classical Borgen plots are limited to nonnegative data and can be constructed for the spectral factor or for the concentration profiles. In the first part of this paper, a simultaneous construction of the two dual Borgen plots is presented, which intensively exploits the underlying duality principles. The...

Read More thumbnail image: Simultaneous construction of dual Borgen plots_ II Algorithmic enhancement for applications to noisy spectral data

The pharmacokinetics study of ginkgolide A, B and the effect of food on bioavailability after oral administration of ginkgolide extracts in beagle dogs

Published: Mar 8, 2018

Author(s): Lixiang Aa, Fei Fei, Zhaoyi Tan, Jiye Aa, Guangji Wang, Changxiao Liu

Journal: Biomedical Chromatography

Abstract Ginkgolides are the primarily active components in Ginkgo products that are popular worldwide. However, few studies have evaluated the bioavailability of ginkgolides and the effects of food on it after oral administration of ginkgolides. In this article, pharmacokinetics and absolute bioavailability of the primary components in ginkgolide extracts were evaluated in beagle dogs. For the first time, we showed that the fed dogs ...

Read More thumbnail image: The pharmacokinetics study of ginkgolide A B and the effect of food on bioavailability after oral administration of ginkgolide extracts in beagle dogs

In Immunopeptidomics We Need a Sniper Instead of a Shotgun

Published: Mar 7, 2018

Author(s): Pouya Faridi, Anthony Wayne Purcell, Nathan Paul Croft

Journal: PROTEOMICS

Abstract Immunopeptidomics employs the use of mass spectrometry to identify and quantify peptides presented on the surface of cells by major histocompatibility complex (MHC; human leukocyte antigen [HLA], in humans) molecules, an essential component of adaptive immunity. Currently, immunopeptidomics follows the same or similar workflows as the more established field of shotgun proteomics, yet inherent differences between these two...

Read More thumbnail image: In Immunopeptidomics We Need a Sniper Instead of a Shotgun

Can we beat overfitting?—A closer look at Cloarec's PLS algorithm

Published: Mar 7, 2018

Author(s): Pedro F. M. Sousa, K. Magnus Åberg

Journal: Journal of Chemometrics

Abstract Random noise has been addressed as a cause of overfitting in partial least squares regression. A previous study pinpointed that one of the sources of overfitting resides in the calculation of scores due to the accumulation of noise in the diagonal of the variance‐covariance matrix, and a modified partial least squares regression was proposed with the removal of this diagonal prior to the score calculation. Here, a further...

Read More thumbnail image: Can we beat overfittingA closer look at Cloarecs PLS algorithm

High‐throughput statistical screening of antiinfective peptides from natural antibacterial protein repertoire: Chemometric prediction, molecular modeling, and susceptibility analysis

Published: Mar 7, 2018

Author(s): Guangmei Sun, Liyun Leng, Xiaocui Wang

Journal: Journal of Chemometrics

Abstract Antibiotic‐resistant bacterial infection (ARBI) is one of the most serious global public health threats. Antiinfective peptides (AIPs) have been recognized as a promising alternative to traditional antibiotics, which can effectively combat the ARBI in a distinct mechanism. In the current study, we attempt to discover new and potent AIPs from the natural antibacterial protein repertoire. Hundreds of antibacterial proteins...

Read More thumbnail image: Highthroughput statistical screening of antiinfective peptides from natural antibacterial protein repertoire Chemometric prediction molecular modeling and susceptibility analysis

The RametrixLITE T oolbox v1.0 for MATLAB ®

Published: Mar 7, 2018

Author(s): Amanda K. Fisher, William F. Carswell, Ahmad I.M. Athamneh, Meaghan C. Sullivan, John L. Robertson, David R. Bevan, Ryan S. Senger

Journal: Journal of Raman Spectroscopy

Abstract To contribute to the growing interest in using Raman spectroscopy to analyze biological samples and provide chemometric analysis, we have developed a Raman Chemometrics (Rametrix™) Toolbox for use with MATLAB®. The LITE version of the Rametrix™ Toolbox is free to academic users through GitHub ( https://github.com/SengerLab/RametrixLITEToolbox) and provides a graphical user interface for application of the following to Raman spectra:...

Read More thumbnail image: The Rametrix  LITE T oolbox v1_0 for MATLAB

Negative ion laser desorption/ionization time‐of‐flight mass spectrometric analysis of small molecules by using nanostructured substrate as matrices

Published: Mar 6, 2018

Author(s): Zian Lin, Zongwei Cai

Journal: Mass Spectrometry Reviews

Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) is an excellent analytical technique for rapid and sensitive analysis of macromolecules such as polymers and proteins. However, the main drawback of MALDI‐TOF MS is its difficulty to detect small molecules with mass below 700 Da because of the intensive interference from MALDI matrix in the low mass region. In recent years...

Read More thumbnail image: Negative ion laser desorptionionization timeofflight mass spectrometric analysis of small molecules by using nanostructured substrate as matrices

Microgradient separation technique for purification and fractionation of permethylated N‐glycans before mass spectrometric analyses

Published: Mar 6, 2018

Author(s): Pavel Rehulka, Martina Zahradnikova, Helena Rehulkova, Petra Dvorakova, Rudolf Nenutil, Dalibor Valik, Borivoj Vojtesek, Lenka Hernychova, Milos V. Novotny

Journal: Journal of Separation Science

Abstract Analysis of N‐glycans released enzymatically from patients’ sera or other clinical samples may provide diagnostically and prognostically important information on human disease. Permethylation of these biomolecules simultaneously increases their hydrophobicity and substantially improves their detection parameters in the following mass spectrometric analyses. The overall procedure, from the glycan cleavage to the final mass...

Read More thumbnail image: Microgradient separation technique for purification and fractionation of permethylated Nglycans before mass spectrometric analyses

Magnetic separation coupled with high‐performance liquid chromatography–mass spectrometry for rapid separation and determination of lignans in Schisandra chinensis

Published: Mar 6, 2018

Author(s): Jishou Piao, Lu Liu, Sihong Wang, Hai‐Bo Shang, Miao He, Ninghai Quan, Donghao Li

Journal: Journal of Separation Science

Abstract Despite the strong antihepatotoxic, antioxidant, and antitumor properties of lignans from Schisandra chinensis, their applications in new drug development, bioscience and functional foods, etc. are limited because of their low abundance and complex coextractions. In this study, a magnetic separation method has been developed based on polyethylenimine‐modified magnetic nanoparticles to rapidly and effectively separate and purify the...

Read More thumbnail image: Magnetic separation coupled with highperformance liquid chromatographymass spectrometry for rapid separation and determination of lignans in Schisandra chinensis

Quantitative assessment of metal dysregulation in β ‐thalassemia patients in comparison with healthy controls by ICP‐MS and chemometric analyses

Published: Mar 5, 2018

Author(s): Sabiha Farooq, Wardah Mazhar, Amna Jabbar Siddiqui, Saqib Hussain Ansari, Syed Ghulam Musharraf

Journal: Biomedical Chromatography

Abstract β‐Thalassemia is one of the most common inherited disorders and is widely distributed throughout the world. Owing to severe deficiencies in red blood cell production, blood transfusion is required to correct anemia for normal growth and development but causes additional complications owing to iron overload. The aim of this study is to quantify the biometal dysregulations in β‐thalassemia patients as compared with healthy...

Read More thumbnail image: Quantitative assessment of metal dysregulation in  thalassemia patients in comparison with healthy controls by ICPMS and chemometric analyses

Plasma phospholipid profiling of a mouse model of anxiety disorder by hydrophilic interaction liquid chromatography coupled to high‐resolution mass spectrometry

Published: Mar 5, 2018

Author(s): Róbert Berkecz, Tímea Körmöczi, Ferenc Tömösi, Viktor Szegedi, János Horváth, Nóra Kovács, Tamás Janáky

Journal: Biomedical Chromatography

Abstract Glycerophospholipids (PLs), as amphipathic small molecules and the main constituents of biological membranes, play an important role in several cellular processes, even though their accurate identification from complex biological samples remains a challenge. In this paper, we report a fast and comprehensive HILIC‐ESI‐MS method for the analysis of glycerophospholipid classes using high‐resolution mass spectrometry in...

Read More thumbnail image: Plasma phospholipid profiling of a mouse model of anxiety disorder by hydrophilic interaction liquid chromatography coupled to highresolution mass spectrometry

Damage accumulation and structural modification in a‐ and c‐plane GaN implanted with 400‐keV and 5‐MeV Au + ions

Published: Mar 2, 2018

Author(s): A. Macková, P. Malinskyˊ, A. Jágerová, Z. Sofer, D. Sedmidubský, K. Klímová, R. Böttger, S. Akhmadaliev

Journal: Surface and Interface Analysis

c‐plane (0001) and a‐plane (11‐20) gallium nitride (GaN) epitaxial layers were grown by Metal organic Vapour Phase epitaxy (MOVPE) on sapphire and subsequently implanted with 400‐keV and 5‐MeV Au+ ions using fluences 5 × 1014 to 5 × 1015 cm−2. The shallow Au depth profiling was accomplished by Rutherford backscattering spectrometry. The structural changes during implantation and subsequent annealing were characterised by...

Read More thumbnail image: Damage accumulation and structural modification in a and cplane GaN implanted with 400keV and 5MeV Au  ions

Chemical state analysis using Auger parameters for XPS spectrum curve fitted with standard Auger spectra

Published: Mar 2, 2018

Author(s): Masahide Shima, Kenichi Tsutsumi, Akihiro Tanaka, Hiroshi Onodera, Masaki Tanemura

Journal: Surface and Interface Analysis

Chemical state analysis is quite important in X‐ray photoelectron spectroscopy. Auger parameter analysis is one of the useful methods to analyze the chemical state in X‐ray photoelectron spectroscopy, because it is not necessary to take the charging effect into account for the analysis of nonconductive materials, especially for the simple material systems of a single chemical state. For the analysis of complicated complex systems, here,...

Read More thumbnail image: Chemical state analysis using Auger parameters for XPS spectrum curve fitted with standard Auger spectra

Co‐implantation of Er and Yb ions into single‐crystalline and nano‐crystalline diamond

Published: Mar 2, 2018

Author(s): Jakub Cajzl, Banu Akhetova, Pavla Nekvindová, Anna Macková, Petr Malinský, Jiří Oswald, Zdeněk Remeš, Marián Varga, Alexander Kromka

Journal: Surface and Interface Analysis

The paper reports on the results of Er‐Yb and Er‐Al co‐implantation into commercial single‐crystalline diamonds as well as into nano‐crystalline diamond (NCD) thin films and their photoluminescence properties. The NCD thin films were deposited on fused silica glass by linear‐antenna microwave plasma‐enhanced chemical vapour deposition (PE MWCVD). Er implantation was performed at an energy of 190 keV and fluences of 1 × 1015...

Read More thumbnail image: Coimplantation of Er and Yb ions into singlecrystalline and nanocrystalline diamond

Simultaneous determination and qualitative analysis of six types of components in Naoxintong capsule by miniaturized matrix solid‐phase dispersion extraction coupled with ultra high‐performance liquid chromatography with photodiode array detection and quadrupole time‐of‐flight mass spectrometry

Published: Mar 2, 2018

Author(s): Huilin Wang, Yan Jiang, Mingya Ding, Jin Li, Jia Hao, Jun He, Hui Wang, Xiu‐Mei Gao, Yan‐Xu Chang

Journal: Journal of Separation Science

Abstract A simple and effective sample preparation process based on miniaturized matrix solid‐phase dispersion was developed for simultaneous determination of phenolic acids (gallic acid, chlorogenic acid, ferulic acid, 3,5‐dicaffeoylqunic acid, 1,5‐dicaffeoylqunic acid, rosmarinic acid, lithospermic acid, and salvianolic acid B), flavonoids (kaempferol‐3‐O‐rutinoside, calycosin, and formononetin), lactones (ligustilide and butyllidephthalide),...

Read More thumbnail image: Simultaneous determination and qualitative analysis of six types of components in Naoxintong capsule by miniaturized matrix solidphase dispersion extraction coupled with ultra highperformance liquid chromatography with photodiode array detection and quadrupole timeofflight mass spectrometry

Quantitative analysis of Yb 4d photoelectron spectrum of metallic Yb

Published: Mar 2, 2018

Author(s): N. Pauly, F. Yubero, S. Tougaard

Journal: Surface and Interface Analysis

The measured Yb 4d3/2 intensity is larger than the Yb 4d5/2 in X‐ray photoelectron (XPS) emission of metallic Yb, which is unexpected. The shape and intensity of photoelectron peaks are strongly affected by extrinsic excitations due to electron transport out of the surface (including bulk and surface effects) and to intrinsic excitations due to the sudden creation of the static core hole. To quantitatively extract from experimental XPS...

Read More thumbnail image: Quantitative analysis of Yb 4d photoelectron spectrum of metallic Yb
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