scholarly journals Lysine Acetylation: Elucidating the Components of an Emerging Global Signaling Pathway in Trypanosomes

2012 ◽  
Vol 2012 ◽  
pp. 1-16 ◽  
Author(s):  
Victoria Lucia Alonso ◽  
Esteban Carlos Serra
Keyword(s):  
Mass Spectrometry ◽  
Rational Design ◽  
High Resolution Mass Spectrometry ◽  
Lysine Acetylation ◽  
Nuclear Compartment ◽  
The Past ◽  
Regulatory Functions ◽  
Potential Use ◽  
Resolution Mass ◽  
Made In

In the past ten years the number of acetylated proteins reported in literature grew exponentially. Several authors have proposed that acetylation might be a key component in most eukaryotic signaling pathways, as important as phosphorylation. The enzymes involved in this process are starting to emerge; acetyltransferases and deacetylases are found inside and outside the nuclear compartment and have different regulatory functions. In trypanosomatids several of these enzymes have been described and are postulated to be novel antiparasitic targets for the rational design of drugs. In this paper we overview the most important known acetylated proteins and the advances made in the identification of new acetylated proteins using high-resolution mass spectrometry. Also, we summarize what is known so far about the acetyltransferases and deacetylases in eukaryotes, focusing on trypanosomes and their potential use as chemotherapeutic targets.

Update on the biological relevance of lysine acetylation as a novel drug target in trypanosomatids

2021 ◽  
Vol 28 ◽  
Author(s):  
Gonzalo Martinez Peralta ◽  
Esteban Serra ◽  
Victoria Lucia Alonso
Keyword(s):  
Signaling Pathways ◽  
Drug Target ◽  
Rational Design ◽  
Review Article ◽  
Lysine Acetylation ◽  
Nuclear Compartment ◽  
Biological Relevance ◽  
Regulatory Functions ◽  
Novel Drug ◽  
Potential Use

: The number of acetylated proteins identified from bacteria to mammals has grown exponentially in the last ten years and it is now accepted that acetylation is a key component in most eukaryotic signaling pathways, as important as phosphorylation. The enzymes involved in this process are well described in mammals; acetyltransferases and deacetylases are found inside and outside the nuclear compartment and have different regulatory functions. In trypanosomatids several of these enzymes have been described and are postulated to be novel antiparasitic targets for the rational design of drugs. In this review article we present an update of the most important known acetylated proteins in trypanosomatids analyzing the acetylomes available. Also, we summarize the information available regarding acetyltransferases and deacetylases in trypanosomes and their potential use as chemotherapeutic targets.

scholarly journals MetaboAnalystR 3.0: Toward an Optimized Workflow for Global Metabolomics

Metabolites ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 186 ◽  
Author(s):  
Zhiqiang Pang ◽  
Jasmine Chong ◽  
Shuzhao Li ◽  
Jianguo Xia
Keyword(s):  
Mass Spectrometry ◽  
High Resolution Mass Spectrometry ◽  
Peak Picking ◽  
Batch Effects ◽  
Spectral Processing ◽  
Activity Prediction ◽  
Pathway Activity ◽  
The Past ◽  
Global Metabolomics ◽  
Resolution Mass

Liquid chromatography coupled to high-resolution mass spectrometry platforms are increasingly employed to comprehensively measure metabolome changes in systems biology and complex diseases. Over the past decade, several powerful computational pipelines have been developed for spectral processing, annotation, and analysis. However, significant obstacles remain with regard to parameter settings, computational efficiencies, batch effects, and functional interpretations. Here, we introduce MetaboAnalystR 3.0, a significantly improved pipeline with three key new features: (1) efficient parameter optimization for peak picking; (2) automated batch effect correction; and (3) more accurate pathway activity prediction. Our benchmark studies showed that this workflow was 20~100× faster compared to other well-established workflows and produced more biologically meaningful results. In summary, MetaboAnalystR 3.0 offers an efficient pipeline to support high-throughput global metabolomics in the open-source R environment.

scholarly journals Historical Exposomics And High Resolution Mass Spectrometry

Exposome ◽  
2021 ◽  
Author(s):  
Dagny Aurich ◽  
Owen Miles ◽  
Emma L Schymanski
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
Data Science ◽  
High Resolution Mass Spectrometry ◽  
Data Interpretation ◽  
The Past ◽  
High Resolution Mass ◽  
Data Archives ◽  
Analytical Approaches ◽  
Resolution Mass

Abstract Awareness of the exposome and its influence on health has increased in the last decade. As past exposures can cause changes in human health many years later, delving into the past is relevant for both diagnostic and prevention purposes, but remains a challenging task. Lifestyle, diet and socioeconomic information of the past should be well documented and compatible with modern data science methods. While chemical analysis nowadays makes use of High Resolution Mass Spectrometry (HR-MS) for highly sensitive and comprehensive coverage of samples plus retrospective analysis, these data archives are in the very early stages. Since past measurements are often only available for a limited set of chemicals, adding to this knowledge requires careful selection of sample types and sampling sites, which may not always be available. The choice of analytes and analytical methods should be suitable for the study question—which is not always clear in advance in exposomics. Data interpretation and the use of appropriate databases are indispensable for a proper exposure assessment, and as databases and knowledge grow, re-analysis of physically or digitally archived samples could enable “continuous monitoring” efforts. This review focusses on the chemical analytical approaches necessary to capture the complexity of the historical exposome. Various sample types, analytes as well as analyses and data interpretation methods are discussed in relation to chemical exposures, while the connection to health remains in focus. It ends with perspectives and challenges in assessing the historical exposome, discussing how we can “learn from the past” to build a better future.

Exploring the Active Compounds of Traditional Mongolian Medicine Agsirga in Intervention of Novel Coronavirus (2019-nCoV) Based on HPLC-Q-Exactive-MS/MS and Molecular Docking Method

2020 ◽  
Author(s):  
Jie Cheng ◽  
Yuchen Tang ◽  
Baoquan Bao ◽  
Ping Zhang
Keyword(s):  
Mass Spectrometry ◽  
Molecular Docking ◽  
High Resolution ◽  
Mass Spectra ◽  
High Resolution Mass Spectrometry ◽  
Structural Formula ◽  
Active Compounds ◽  
High Resolution Mass ◽  
Q Exactive ◽  
Resolution Mass

<p><a></a><a></a><a></a><a><b>Objective</b></a>: To screen all compounds of Agsirga based on the HPLC-Q-Exactive high-resolution mass spectrometry and find potential inhibitors that can respond to 2019-nCoV from active compounds of Agsirga by molecular docking technology.</p> <p><b>Methods</b>: HPLC-Q-Exactive high-resolution mass spectrometry was adopted to identify the complex components of Mongolian medicine Agsirga, and separated by the high-resolution mass spectrometry Q-Exactive detector. Then the Orbitrap detector was used in tandem high-resolution mass spectrometry, and the related molecular and structural formula were found by using the chemsipider database and related literature, combined with precise molecular formulas (errors ≤ 5 × 10<sup>−6</sup>) , retention time, primary mass spectra, and secondary mass spectra information, The fragmentation regularities of mass spectra of these compounds were deduced. Taking ACE2 as the receptor and deduced compounds as the ligand, all of them were pretreated by discover studio, autodock and Chem3D. The molecular docking between the active ingredients and the target protein was studied by using AutoDock molecular docking software. The interaction between ligand and receptor is applied to provide a choice for screening anti-2019-nCoV drugs.</p> <p><b>Result</b>: Based on the fragmentation patterns of the reference compounds and consulting literature, a total of 96 major alkaloids and stilbenes were screened and identified in Agsirga by the HPLC-Q-Exactive-MS/MS method. Combining with molecular docking, a conclusion was got that there are potential active substances in Mongolian medicine Agsirga which can block the binding of ACE2 and 2019-nCoV at the molecular level.</p>

Determination of quaternary ammonium compounds in food products by the method of ultra-performance liquid chromatography/high resolution mass-spectrometry

2020 ◽  
Vol 86 (8) ◽  
pp. 23-31
Author(s):  
V. G. Amelin ◽  
D. S. Bolshakov
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
Quaternary Ammonium ◽  
High Resolution Mass Spectrometry ◽  
Food Products ◽  
Quaternary Ammonium Compounds ◽  
High Resolution Mass ◽  
Ammonium Compounds ◽  
Resolution Mass

The goal of the study is developing a methodology for determination of the residual amounts of quaternary ammonium compounds (QAC) in food products by UHPLC/high-resolution mass spectrometry after water-acetonitrile extraction of the determined components from the analyzed samples. The identification and determination of QAC was carried out on an «UltiMate 3000» ultra-high-performance liquid chromatograph (Thermo Scientific, USA) equipped with a «maXis 4G» high-resolution quadrupole-time-of-flight mass spectrometric detector and an ion spray «ionBooster» source (Bruker Daltonics, Germany). Samples of milk, cheese (upper cortical layer), dumplings, pork, chicken skin and ground beef were used as working samples. Optimal conditions are specified for chromatographic separation of the mixture of five QAC, two of them being a mixture of homologues with a linear structure (including isomeric forms). The identification of QAC is carried out by the retention time, exact mass of the ions, and coincidence of the mSigma isotopic distribution. The limits for QAC detection are 0.1 – 0.5 ng/ml, the determination limits are 1 ng/ml for aqueous standard solutions. The determinable content of QAC in food products ranges within 1 – 100 ng/g. The results of analysis revealed the residual amount of QAC present in all samples, which confirms data of numerous sources of information about active use of QAC-based disinfectants in the meat and dairy industry. The correctness of the obtained results is verified by introduction of the additives in food products at a level of 10 ng/g for each QAC. The relative standard deviation of the analysis results does not exceed 0.18. The duration of the analysis is 30 – 40 min.

Measuring Exposome Associated with Health

2020 ◽  
pp. 46-50
Keyword(s):  
Mass Spectrometry ◽  
Remote Sensing ◽  
High Resolution ◽  
Biological Effect ◽  
High Resolution Mass Spectrometry ◽  
The Body ◽  
Ecological Environment ◽  
Special Issue ◽  
The Life Course ◽  
Resolution Mass

The concept of exposome has received increasing discussion, including the recent Special Issue of Science –"Chemistry for Tomorrow's Earth,” about the feasibility of using high-resolution mass spectrometry to measure exposome in the body, and tracking the chemicals in the environment and assess their biological effect. We discuss the challenges of measuring and interpreting the exposome and suggest the survey on the life course history, built and ecological environment to characterize the sample of study, and in combination with remote sensing. They should be part of exposomics and provide insights into the study of exposome and health.

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