Structural Insights into Plant Viruses Revealed by Small-Angle X-ray Scattering and Atomic Force Microscopy.

The structural study of plant viruses is of great importance to reduce the damage caused by these agricultural pathogens and to support their biotechnological applications. Nowadays, X-ray crystallography, NMR spectroscopy and cryo-electron microscopy are well accepted methods to obtain the 3D protein structure with the best resolution. However, for large and complex supramolecular structures such as plant viruses, especially flexible filamentous ones, there are a number of technical limitations to resolving their native structure in solution.

A comparative study of the predictive performance of different descriptor calculation tools: Molecular-based elution order modeling and interpretation of retention mechanism for isomeric compounds from METLIN database.

In the pharmaceutical industry, the need for analytical standards is a bottleneck for comprehensive evaluation and quality control of intermediate and end products. These are complex mixtures containing structurally related molecules. In this regard, chromatographic peak annotation, especially for critical pairs of isomers and closest structural analogs, can be supported by using a Quantitative Structure Retention Relationship (QSRR) approach.

CKD Urine Metabolomics: Modern Concepts and Approaches.

One of the primary challenges regarding chronic kidney disease (CKD) diagnosis is the absence of reliable methods to detect early-stage kidney damage. A metabolomic approach is expected to broaden the current diagnostic modalities by enabling timely detection and making the prognosis more accurate. Analysis performed on urine has several advantages, such as the ease of collection using noninvasive methods and its lower protein and lipid content compared with other bodily fluids.

Analysis of Primary Liquid Chromatography Mass Spectrometry Data by Neural Networks for Plant Samples Classification.

Plant samples are potential sources of physiologically active secondary metabolites and their classification is an extremely important task in traditional medicine and other fields of research. In the production of herbal drugs, different plant parts of the same or related species can serve as adulterants for primary plant material. The use of highly informative and relatively easily accessible tools, such as liquid chromatography and low-resolution mass spectrometry, helps to solve these tasks by means of fingerprint analysis.

An application of the standardised reference extract quantification strategy in the quality control of ginseng infusions by liquid chromatography with mass spectrometric detection.

Introduction: Limited availability of individual standards is a bottleneck for quality control of functional foods and natural medicines. The use of standard mixtures or secondary standards is a possible alternative in this case. Earlier, an approach known as standardised reference extract (RE) strategy was introduced for HPLC-UV analysis of different plant materials; however, its application in HPLC-MS analysis has not been investigated.

Deep learning for retention time prediction in reversed-phase liquid chromatography.

Retention time prediction in high-performance liquid chromatography (HPLC) is the subject of many studies since it can improve the identification of unknown molecules in untargeted profiling using HPLC coupled with high-resolution mass spectrometry. Lots of approaches were developed for retention time prediction in liquid chromatography for a different number of molecules considering various molecular properties and machine learning algorithms. The recently built large retention time data set of standard compounds from the Metabolite and Chemical Entity Database (METLIN) allows researchers to create a model that can be used for retention time prediction of small molecules with wide varieties of structures and physicochemical properties.

Unsupervised methods in LC-MS data treatment: Application for potential chemotaxonomic markers search.

The combination of Liquid Chromatography and Mass Spectrometry (LC-MS) is commonly used to determine and characterize biologically active compounds because of its high resolution and sensitivity. In this work we explore the interpretation of LC-MS data using multivariate statistical analysis algorithms to extract useful chemical information and identify clusters of similar samples. Samples of leaves from 19 plants belonging to the Apiaceae family were analyzed in unified LC conditions by high- and low-resolution mass spectrometry in a wide range scan mode.

A novel simple and sensitive approach for determination of 1,1-dimethylhydrazine in aqueous samples by high performance liquid chromatography with ultraviolet and tandem mass spectrometric detection after derivatization with unsubstituted aromatic aldehydes.

In this work, simple, rapid and highly sensitive method of hazardous chemical 1,1-dimethylhydrazine (unsymmetrical dimethylhydrazine, UDMH) determination based on pre-column derivatization with unsubstituted aromatic aldehydes and reversed-phase high performance liquid chromatography-ultraviolet-tandem mass spectrometry (RP HPLC-UV-MS/MS) has been developed. Along with benzaldehyde, commercially available aromatic aldehydes, namely: 2-naphthaldehyde, 2-pyridinecarboxaldehyde, and 2-quinolinecarboxaldehyde, were used as derivatizing reagents in the analysis of hydrazines for the first time. The reactions were studied in a wide pH range by varying reaction time and other conditions.

Quantitative aspects of the hydrolysis of ginseng saponins: Application in HPLC-MS analysis of herbal products.

Background: Ginseng is one of the most valuable herbal supplements. It is challenging to perform quality control of ginseng products due to the diversity of bioactive saponins in their composition. Acid or alkaline hydrolysis is often used for the structural elucidation of these saponins and sugars in their side chains.

A new PARAFAC-based algorithm for HPLC-MS data treatment: herbal extracts identification.

Introduction: Role of highly informative high-performance liquid chromatography mass spectrometry (HPLC-MS) methods in quality control is increasing. Complex herbal products and formulations can simultaneously contain extracts from different plants. Therefore, due to the leads to lack of commercial standards it is important to develop novel approaches for comprehensive treatment of big datasets.

A classification of liquid chromatography mass spectrometry techniques for evaluation of chemical composition and quality control of traditional medicines.

Natural products (NPs) and traditional medicines (TMs) are used for treatment of various diseases and also to develop new drugs. However, identification of drug leads within the immense biodiversity of living organisms is a challenging task that requires considerable time, labor, and computational resources as well as the application of modern analytical instruments. LC-MS platforms are widely used for both drug discovery and quality control of TMs and food supplements.

Nerve agent markers screening after accumulation in garden cress (Lepidium sativum) used as a model plant object.

In this research an accumulation of nerve agent markers in garden cress (Lepidium sativum) as a model plant object was studied using LC-QTOF hybrid system. For the determination of methylphosphonic acid and alkyl methylphosphonates, which are specific markers of sarin, soman, VR and VX, simple and sensitive approach was developed. Direct analysis of aqueous extracts on the reversed phase column with polar endcapping allowed to achieve satisfactory retention factor for methylphosphonic acid, which has high polarity and is usually very weakly retained on the ordinary reversed phase columns.

Application of quantitative analysis of multi-component system approach for determination of ginsenosides in different mass-spectrometric conditions.

The lack of standard substances is a bottleneck for quality control in traditional and alternative medicine. Development of the HPLC-UV approaches combined with single standard for quantitative analysis of multi-component system (QAMS) allowed determination of several plant biomarkers by implementation of the relative response factors (RRFs). Robustness and ruggedness of such methods are commonly demonstrated by performing the analysis in changing analytical conditions on the different HPLC equipment and columns.

Unified strategy for HPLC-MS evaluation of bioactive compounds for quality control of herbal products.

Evaluation of safety, quality and composition of herbal products and food supplements based on botanical ingredients is a matter of serious concern. For screening of botanicals in herbal products multitargeted and group-targeted approaches may be applied. In the group-targeted approach botanicals are characterized by means of an appropriate group of structurally related biomarkers compared with the multitargeted approach where a number of selected analytes are monitored based on a multiple reaction monitoring survey.

Impact of weak water deficit on growth, photosynthetic primary processes and storage processes in pine and spruce seedlings.

We investigated the influence of 40 days of drought on growth, storage processes and primary photosynthetic processes in 3-month-old Scots pine and Norway spruce seedlings growing in perlite culture. Water stress significantly affected seedling water status, whereas absolute dry biomass growth was not substantially influenced. Water stress induced an increase in non-structural carbohydrate content (sugars, sugar alcohols, starch) in the aboveground part of pine seedlings in contrast to spruce seedlings.

LC-MS determination of steroidal glycosides from Dioscorea deltoidea Wall cell suspension culture: Optimization of pre-LC-MS procedure parameters by Latin Square design.

In this paper, the ultrasound assisted extraction method for isolation of steroidal glycosides from D. deltoidea plant cell suspension culture with a subsequent HPLC-MS determination was developed. After the organic solvent was selected via a two-factor experiment the optimization via Latin Square 4 × 4 experimental design was carried out for the following parameters: extraction time, organic solvent concentration in extraction solution and the ratio of solvent to sample.

Binding and Action of Amino Acid Analogs of Chloramphenicol upon the Bacterial Ribosome.

Antibiotic chloramphenicol (CHL) binds with a moderate affinity at the peptidyl transferase center of the bacterial ribosome and inhibits peptide bond formation. As an approach for modifying and potentially improving properties of this inhibitor, we explored ribosome binding and inhibitory activity of a number of amino acid analogs of CHL. The L-histidyl analog binds to the ribosome with the affinity exceeding that of CHL by 10 fold.

Structure elucidation of sweet-tasting cycloartane-type saponins from ginseng oolong tea and Abrus precatorius L. leaves.

The composition of ginseng oolong a widely used tea product was investigated. A new sweet-tasting cycloartane-type saponin 3β-O-[β-D-glucuronopyranosyl(1→2)]-β-D-6-acetylglucopyranosyl)-(20S,22S)-3β,22-dihydroxy-9,19-cyclolanost-24-en-26,29-oic acid (9), along with five new compounds, was identified in the methanolic extract of the ginseng oolong tea. Structural elucidation was conducted by spectroscopic methods, including 1D- and 2D-NMR, HR-MS, HPLC-LITMS/MS.

Rapid IC-MS/MS determination of methylphosphonic acid in urine of rats exposed to organophosphorus nerve agents.

A direct approach for the determination of a specific hydrolysis product of organophosphorus nerve agents such as methylphosphonic acid (MPA) in urine by ion chromatography and tandem mass spectrometry (IC-MS/MS) has been developed. The first advantage of the proposed approach is a rapid and simple sample preparation, which does not require a large sample volume, complicated and laborious preconcentration and derivatization steps, and takes less than 7min per sample. The second advantage is the fast and selective IC determination of MPA carried out on a noncommercial anion exchanger based on a poly(styrene-co-divinylbenzene) (PS-DVB) substrate with a high degree of crosslinking and a covalently-bonded branched functional layer, which enables complete resolution of MPA from major urine matrix components and allows one to overcome matrix effects.

Combination of HPLC-MS and QAMS as a new analytical approach for determination of saponins in ginseng containing products.

Conventional liquid chromatographic methods coupled with ultraviolet detection with low-wavelength range are lacking selectivity and sensitivity to determine both polar and less polar ginsenosides. Also the lack of standard substances for such quality control methods is leading to development of the approaches using single standard for quantitative analysis of multi-component system (QAMS). The objective of present study was to establish and compare for the first time liquid chromatography-ultraviolet detection and liquid chromatography-mass spectrometry QAMS methods for the simultaneous determination of protopanaxatriol-type and protopanaxadiol-type ginsenosides in a variety of ginseng products.

"Dilute-and-shoot" rapid-separation liquid chromatography tandem mass spectrometry method for fast detection of thiodiglycolic acid in urine.

A new sensitive rapid-separation liquid chromatography tandem mass spectrometry approach for the determination of thiodiglycolic acid (TDGA) in urine has been developed. The use of the "dilute-and-shoot" method helps to shorten the sample preparation stage and provides a sensitive and direct approach for TDGA determination in urine. Chromatographic separation of the analyte and other urine compounds was achieved using a reverse-phase liquid chromatography column with mobile phases consisting of 0.

Single-run HPLC/ESI-LITMS profiling of ginsenosides in plant extracts and ginseng based products.

A rapid single-run analytical approach suitable to achieve a comprehensive characterization of ginsenosides - the main bioactive compounds present in plant materials from Panax species and ginseng-based products - was developed. The method is based on high-performance liquid chromatography coupled with electrospray positive ionization linear ion trap mass spectrometry (HPLC/ESI-LITMS). The main ions in the ESI-LITMS spectra were attributed to molecular adducts with sodium and potassium and fragments corresponding to cleavage of the glycosidic bonds.

'Dilute-and-shoot' RSLC-MS-MS method for fast detection of nerve and vesicant chemical warfare agent metabolites in urine.

A sensitive screening method based on fast liquid chromatography tandem mass-spectrometry (RSLC-MS-MS) has shown the feasibility of separation and detection of low concentration β-lyase metabolites of sulfur mustard and of nerve agent phosphonic acids in urine. The analysis of these compounds is of interest because they are specific metabolites of the chemical warfare agents (CWAs), sulfur mustard (HD), sarin (GB), soman (GD), VX and Russian VX (RVX). The 'dilute-and-shoot' RSLC-MS-MS method provides a sensitive and direct approach for determining CWA exposure in non-extracted non-derivatized samples from urine.

A validated LC-MS/MS method for rapid determination of methotrexate in human saliva and its application to an excretion evaluation study.

A sensitive and simple method for the methotrexate quantification was developed using aminopterin as internal standard. Methotrexate is an anticancer agent that is widely used in a variety of human cancers including primary central nervous system lymphoma. The compound was quantified by liquid-chromatography coupled to electrospray ionization (positive ion-mode) low-energy collision dissociation-tandem mass spectrometry.