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Updates on resources, software tools, and databases for plant proteomics in 2016–2017

Published: Mar 1, 2018

Author(s): Biswapriya B. Misra

Journal: ELECTROPHORESIS

Abstract Proteomics data processing, annotation, and analysis can often lead to major hurdles in large‐scale high‐throughput bottom‐up proteomics experiments. Given the recent rise in protein‐based big datasets being generated, efforts in in silico tool development occurrences have had an unprecedented increase; so much so, that it has become increasingly difficult to keep track of all the advances in a particular academic year. However, these...

Read More thumbnail image: Updates on resources software tools and databases for plant proteomics in 20162017

Topics in chemometrics, TIC 2017, a personal report

Published: Feb 28, 2018

Author(s): Marcel Maeder

Journal: Journal of Chemometrics

Read More thumbnail image: Topics in chemometrics TIC 2017 a personal report

kNN based on probability density for fault detection in multimodal processes

Published: Feb 28, 2018

Author(s): Jinyu Guo, Xin Wang, Yuan Li

Journal: Journal of Chemometrics

Abstract Recently, k‐nearest neighbor rules (kNN) have drawn increasing attention for fault detection of multimodal industrial processes. However, the traditional kNN method performs poorly for weak faults in a dense mode when the dispersion degree of each mode is quite different. The reason is that the kNN statistics of weak faults are usually submerged by those of normal data in a mode with a high dispersion degree. To improve the...

Read More thumbnail image: kNN based on probability density for fault detection in multimodal processes

Challenges and emergent solutions for LC‐MS/MS based untargeted metabolomics in diseases

Published: Feb 27, 2018

Author(s): Liang Cui, Haitao Lu, Yie Hou Lee

Journal: Mass Spectrometry Reviews

In the past decade, advances in liquid chromatography‐mass spectrometry (LC‐MS) have revolutionized untargeted metabolomics analyses. By mining metabolomes more deeply, researchers are now primed to uncover key metabolites and their associations with diseases. The employment of untargeted metabolomics has led to new biomarker discoveries and a better mechanistic understanding of diseases with applications in...

Read More thumbnail image: Challenges and emergent solutions for LCMSMS based untargeted metabolomics in diseases

Diffusion MRI visualization

Published: Feb 27, 2018

Author(s): Thomas Schultz, Anna Vilanova

Journal: NMR in Biomedicine

Modern diffusion magnetic resonance imaging (dMRI) acquires intricate volume datasets and biological meaning can only be found in the relationship between its different measurements. Suitable strategies for visualizing these complicated data have been key to interpretation by physicians and neuroscientists, for drawing conclusions on brain connectivity and for quality control. This article provides an overview of visualization solutions...

Read More thumbnail image: Diffusion MRI visualization

Untargeted profiling of Glycyrrhiza glabra extract with comprehensive two‐dimensional liquid chromatography‐mass spectrometry using multi‐segmented shift gradients in the second dimension: Expanding the metabolic coverage

Published: Feb 27, 2018

Author(s): Yong Foo Wong, Francesco Cacciola, Soraya Fermas, Solange Riga, Darryl James, Valeria Manzin, Brice Bonnet, Philip John Marriott, Paola Dugo, Luigi Mondello

Journal: ELECTROPHORESIS

Abstract Metabolic profiling of Glycyrrhiza glabra using comprehensive two‐dimensional liquid chromatography (LC × LC) coupled with photodiode array (PDA) and mass spectrometry (MS) detection is described. The separation was conducted under reversed‐phase conditions, using a combination of first dimension (1D) 150 mm microbore cyano column utilising 2.7 μm diameter (dp) particles, and second dimension (2D) 50 mm...

Read More thumbnail image: Untargeted profiling of Glycyrrhiza glabra extract with comprehensive twodimensional liquid chromatographymass spectrometry using multisegmented shift gradients in the second dimension Expanding the metabolic coverage

Feasibility of peak volume algorithm in electrothermal vaporization microwave plasma atomic emission spectrometry

Published: Feb 27, 2018

Author(s): Jin Shan, Wei Jin, Bingwen Yu, Yangwei Ying, Dan Zhu, Haixiang Yu, Yuwei Yan, Qinhan Jin

Journal: Journal of Chemometrics

Abstract Electro‐thermal vaporization has served as an alternative sample introduction method in atomic spectrometry for some time and provided a better solution for quick analysis of complicated samples because of its high sensitivity and effective separation of analyte from matrix materials. The quick heating process produces sharp signals that can provide much better limits of detection with significant improvements compared with...

Read More thumbnail image: Feasibility of peak volume algorithm in electrothermal vaporization microwave plasma atomic emission spectrometry

Material data mining in Nianyi Chen's scientific family

Published: Feb 27, 2018

Author(s): Wencong Lu, Wei Lv, Qing Zhang, Kailiang Lu, Xiaobo Ji

Journal: Journal of Chemometrics

Abstract The origin of the material data mining (MDM) field in China can be traced back to Professor Nianyi Chen's pioneering contributions in the 80s of the 20th century. His scientific protégés have inherited his research legacy and been continuously pursuing research in this field. The present article provides an overview on the MDM research conducted by Nianyi Chen's scientific family, by reviewing these achievements of the...

Read More thumbnail image: Material data mining in Nianyi Chens scientific family

Computational Tools for the Identification and Interpretation of Sequence Motifs in Immunopeptidomes

Published: Feb 26, 2018

Author(s): Bruno Alvarez, Carolina Barra, Morten Nielsen, Massimo Andreatta

Journal: PROTEOMICS

Abstract Recent advances in proteomics and mass‐spectrometry have widely expanded the detectable peptide repertoire presented by major histocompatibility complex (MHC) molecules on the cell surface, collectively known as the immunopeptidome. Finely characterizing the immunopeptidome brings about important basic insights into the mechanisms of antigen presentation, but can also reveal promising targets for vaccine development and...

Read More thumbnail image: Computational Tools for the Identification and Interpretation of Sequence Motifs in Immunopeptidomes

The analysis of alpha‐1‐antitrypsin glycosylation with direct LC‐MS/MS

Published: Feb 26, 2018

Author(s): Haidi Yin, Mingrui An, Pui‐kin So, Melody Yee‐Man Wong, David M. Lubman, Zhongping Yao

Journal: ELECTROPHORESIS

Abstract A liquid chromatography‐tandem mass spectrometry (LC‐MS/MS)‐based methodology has been developed to differentiate core‐ and antennary‐fucosylated glycosylation of glycopeptides. Both the glycosylation sites (heterogeneity) and multiple possible glycan occupancy at each site (microheterogeneity) can be resolved via intact glycopeptide analysis. The serum glycoprotein alpha‐1‐antitrypsin (A1AT) which contains both core‐ and...

Read More thumbnail image: The analysis of alpha1antitrypsin glycosylation with direct LCMSMS

2DE Gels: A Story of Love and Hate in Proteomics

Published: Feb 23, 2018

Author(s): Daniel Martins‐de‐Souza

Journal: PROTEOMICS

Read More thumbnail image: 2DE Gels A Story of Love and Hate in Proteomics

Latest advances in the extraction and determination of saffron apocarotenoids

Published: Feb 23, 2018

Author(s): Anastasia Kyriakoudi, Maria Z. Tsimidou

Journal: ELECTROPHORESIS

Abstract Saffron, the dried red stigmas of Crocus sativus L. plant, is the most expensive spice in the world. It is highly valued not only for the color and flavor that exerts to various foods and drinks but also for its functional properties. Various classes of apocarotenoids such as crocetin sugar esters, picrocrocin and safranal are responsible for these characteristics. In the present review, the evolution of the methods ...

Read More thumbnail image: Latest advances in the extraction and determination of saffron apocarotenoids

The Role of Mass Spectrometry and Proteogenomics in the Advancement of HLA Epitope Prediction

Published: Feb 23, 2018

Author(s): Amanda L. Creech, Ying S. Ting, Scott P. Goulding, John F.K. Sauld, Dominik Barthelme, Michael S. Rooney, Terri A. Addona, Jennifer G. Abelin

Journal: PROTEOMICS

Abstract A challenge in developing personalized cancer immunotherapies is the prediction of putative cancer‐specific antigens. Currently, predictive algorithms are used to infer binding of peptides to human leukocyte antigen (HLA) heterodimers to aid in the selection of putative epitope targets. One drawback of current epitope prediction algorithms is that they are trained on datasets containing biochemical HLA‐peptide binding data...

Read More thumbnail image: The Role of Mass Spectrometry and Proteogenomics in the Advancement of HLA Epitope Prediction

Specific T Cell Responses against Minor Histocompatibility Antigens Cannot Generally Be Explained by Absence of Their Allelic Counterparts on the Cell Surface

Published: Feb 23, 2018

Author(s): Helena M. Bijen, Chopie Hassan, Michel G. D. Kester, George M. C. Janssen, Pleun Hombrink, Arnoud H. Ru, Jan Wouter Drijfhout, Hugo D. Meiring, Ad P. Jong, J. H. Frederik Falkenburg, Connie R. Jimenez, Mirjam H. M. Heemskerk, Peter A. Veelen

Journal: PROTEOMICS

Abstract Allogeneic stem cell transplantation has emerged as immunotherapy in the treatment of a variety of hematological malignancies. Its efficacy depends on induction of graft versus leukemia by donor lymphocytes. Both graft versus leukemia and graft versus host disease are induced by T cells reactive against polymorphic peptides, called minor histocompatibility antigens (MiHA), which differ between patient and donor and are...

Read More thumbnail image: Specific TCell Responses against Minor Histocompatibility Antigens Cannot Generally Be Explained by Absence of Their Allelic Counterparts on the Cell Surface

Sensitive and rapid determination of pyrethroids in human blood by gas chromatography–tandem mass spectrometry with ultrasound‐assisted dispersive liquid‐liquid microextraction

Published: Feb 23, 2018

Author(s): Xue Gao, Hao Guo, Junwei Wang, Qingbiao Zhao

Journal: Drug Testing and Analysis

Abstract In this study, a sensitive and fast procedure of ultrasonic‐assisted dispersive liquid‐liquid microextraction (UADLLME) coupled with gas chromatography–tandem mass spectrometry (GC–MS/MS) for the determination of major pyrethroid pesticides (permethrin, tetramethrin, bifenthrin, fenvalerate, flucythrinate, fluvalinate, fenpropathrin, deltamethrin, and cyhalothrin) in blood samples was developed. Response surface methodology...

Read More thumbnail image: Sensitive and rapid determination of pyrethroids in human blood by gas chromatographytandem mass spectrometry with ultrasoundassisted dispersive liquidliquid microextraction

The chemistry and pharmacology of synthetic cannabinoid SDB‐006 and its regioisomeric fluorinated and methoxylated analogs

Published: Feb 23, 2018

Author(s): Samuel D. Banister, Alexander Olson, Matthew Winchester, Jordyn Stuart, Amelia R. Edington, Richard C. Kevin, Mitchell Longworth, Marco Herrera, Mark Connor, Iain S. McGregor, Roy R. Gerona, Michael Kassiou

Journal: Drug Testing and Analysis

Abstract Synthetic cannabinoids are the largest and most structurally diverse class of new psychoactive substances, with manufacturers often using isomerism to evade detection and circumvent legal restriction. The regioisomeric methoxy‐ and fluorine‐substituted analogs of SDB‐006 (N‐benzyl‐1‐pentyl‐1H‐indole‐3‐carboxamide) were synthesized and could not be differentiated by gas chromatography–mass spectrometry (GC–MS), but were...

Read More thumbnail image: The chemistry and pharmacology of synthetic cannabinoid SDB006 and its regioisomeric fluorinated and methoxylated analogs

Comparative pharmacokinetics of trandolapril, its active metabolite, and verapamil in human plasma of Egyptian population using HPLC–MS/MS

Published: Feb 23, 2018

Author(s): Ragaa Magdy, Ahmed H. El‐Khatib, Ahmed Hemdan, Omar Abd Elaziz, Maha Farouk, Michael W. Linscheid

Journal: Drug Testing and Analysis

Abstract Trandolapril and verapamil are commonly used antihypertensive drugs. However, there is a lack of available data on the change of their pharmacokinetics in patients with liver or kidney impairment and hence the need for dose adjustment. In this article, a high performance liquid chromatography–tandem mass spectrometry (HPLC–MS/MS) method was developed and validated for the monitoring of trandolapril, its active metabolite...

Read More thumbnail image: Comparative pharmacokinetics of trandolapril its active metabolite and verapamil in human plasma of Egyptian population using HPLCMSMS

Removal of brilliant green and malachite green from aqueous solution by a viable magnetic polymeric nanocomposite: Simultaneous spectrophotometric determination of 2 dyes by PLS using original and first derivative spectra

Published: Feb 20, 2018

Author(s): Maryam Bagtash, Javad Zolgharnein

Journal: Journal of Chemometrics

Abstract Here, we describe the successful synthesis of a new magnetic nanocomposite and investigate simultaneous removal of 2 cationic dyes, brilliant green (BG) and malachite green (MG), from aqueous solutions. The nanocomposite is characterized by scanning electron microscopy, energy‐dispersive X‐ray spectroscopy, thermal gravimetric analysis, and Fourier‐transform infrared spectrophotometry. The spectra of BG and MG in their mixture show...

Read More thumbnail image: Removal of brilliant green and malachite green from aqueous solution by a viable magnetic polymeric nanocomposite Simultaneous spectrophotometric determination of 2 dyes by PLS using original and first derivative spectra

Correlation and redundancy on machine learning performance for chemical databases

Published: Feb 19, 2018

Author(s): Hongzhi Li, Wenze Li, Xuefeng Pan, Jiaqi Huang, Ting Gao, LiHong Hu, Hui Li, Yinghua Lu

Journal: Journal of Chemometrics

Abstract Variable reduction is an essential step for establishing a robust, accurate, and generalized machine learning model. Variable correlation and redundancy/total correlation are the primary considerations in many variable reduction methods given that they directly impact model performances. However, their effects vary from one class of databases to another. To clarify their effects on regression models on the basis of small...

Read More thumbnail image: Correlation and redundancy on machine learning performance for chemical databases

Selective extraction of high‐value phenolic compounds from distillation wastewater of basil ( Ocimum basilicum L.) by pressurized liquid extraction

Published: Feb 16, 2018

Author(s): Imma Pagano, Andrea del Pilar Sánchez‐Camargo, Jose Antonio Mendiola, Luca Campone, Alejandro Cifuentes, Luca Rastrelli, Elena Ibañez

Journal: ELECTROPHORESIS

Abstract During the essential oil steam distillation from aromatic herbs, huge amounts of distillation wastewaters (DWWs) are generated. These by‐products represent an exceptionally rich source of phenolic compounds such as rosmarinic acid (RA) and caffeic acid (CA). Herein, the alternative use of dried basil DWWs (dDWWs) to perform a selective extraction of RA and CA by pressurized liquid extraction (PLE) employing bio‐based...

Read More thumbnail image: Selective extraction of highvalue phenolic compounds from distillation wastewater of basil  Ocimum basilicum L_ by pressurized liquid extraction
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