Quantitative structure retention relationship (QSRR) modelling for Analytes' retention prediction in LC-HRMS by applying different Machine Learning algorithms and evaluating their performance.

In metabolomics, retention prediction methods have been developed based on the structural and physicochemical characteristics of analytes. Such methods employ regression models, harnessing machine learning algorithms mapping experimentally derived retention time (tR) analytes with various structural and physicochemical descriptors, known as Quantitative Structure Retention Relationships (QSRR) models. In the present study, QSRR models have been developed by applying four Machine Learning regression algorithms, i.e. Bayesian Ridge Regression (BRidgeR), Extreme Gradient Boosting Regression (XGBR) and Support Vector Regression (SVR) using both linear and non-linear kernels, all tested and compared for their retention prediction ability on experimentally derived and on publicly available chromatographic data, using Molecular Descriptors to describe the physical, chemical or structural properties of molecules. Various configurations of the available datasets, in terms of the highly-correlated features levels (defined as the maximum absolute value of the Pearson's correlation coefficient calculated between any pair of features) they contained, were analyzed in parallel. This is the first study, to the best of our knowledge, of the effect of collinearity on the performance of QSRR predictive models. In the vast majority of cases studied there was no statistically significant difference in the performance of the generated QSRR predictive models among the specified dataset configurations, indicative of the ability of the selected regression algorithms to effectively handle collinearity. In terms of the individual performance of the selected regression algorithms, no pattern was found where one algorithm (or class of algorithms) stood out significantly relative to the others among the study datasets.

Analysis of urinary organic acids by gas chromatography tandem mass spectrometry method for metabolic profiling applications.

A sensitive, accurate and precise method was developed for the quantification of a large number of organic acids in human urine by GC-MS/MS. The analytes were selected based on their role as key metabolic intermediates; intermediates of Krebs cycle, fatty acid oxidation, glycolysis, down-stream metabolites of neurotransmitter synthesis and degradation, metabolites indicative of nutritional deficiencies, byproducts of microbial activity in the gastrointestinal tract (GI) etc. The most efficient sample preparation protocol was selected based on tests for extraction with different solvents such as MTBE and ethyl acetate under acidic conditions, whereas finally a more general protocol was applied with methanol. Regarding derivatization, methoxyamine with MSTFA, 1% TMCS was applied. The method was extensively validated, including stability study, ensuring accurate determination of the studied organic acids in human urine. Proof of its utility was exhibited in a set of samples from human volunteers. The method can find wide applicability in the context of metabolomics for clinical or nutritional studies.

Biodegradation of expanded polystyrene by mealworm larvae under different feeding strategies evaluated by metabolic profiling using GC-TOF-MS.

The present study investigated the biodegradation of polystyrene (PS) plastic by mealworm (Tenebrio molitor) on different diets followed by untargeted screening of larvae gut intestine tissue and frass (manure and feed residuals) to investigate the existence of polymer-generated organic residues. Three different diets, consisting of PS, rolled barley and water were tested. PS degradation rates ranged from 16% to 23% within 15 days, with no statistical differences in survival rates. The larvae fed with ad libitum barley:PS (20:1 w/w) and water had the highest growth rate, while higher PS consumption was observed for barley:PS of 4:1 w/w. A GC-TOF-MS analysis revealed no contaminating substances in the gut intestine tissue, nor styrene or PS oligomers, whilst several bioactive compounds and traces of alkanes, mostly with small carbon chains, were present. Metabolomics analysis on the collected frass, either on the lipophilic (CHCl3) or the polar fraction (MeOH-H2O) was performed. Styrene and PS oligomers (dimers, trimers) were identified, though in a relatively low total amount, up to a total of 346.0 ng/mg 2,4 di-tert butylphenol was identified in both frass and tissue, coming from the PS polymer (Non-intentionally added substances; NIAS). Finally, in the polar fraction of frass, bioactive molecules (fatty acids, amides) were identified, together with several hydrocarbons, mostly with longer carbon chains. The formation of these substances indicated enzymatic and biochemical activity in the larvae-gut intestine. It was shown that degrading and contaminating organic compounds occur at low levels, in both gut intestine and frass, during bio-degradation of PS.

Targeted urine metabolomics in preterm neonates with intraventricular hemorrhage.

Intraventricular hemorrhage (IVH) is a major cause of morbidity and mortality in preterm neonates. Elucidation of the mechanisms underlying IVH and/or development of disease biomarkers is essential. The aim of the study was to investigate the urine metabolic profile of preterm neonates (gestational age < 32 weeks) IVH and explore the role of metabolomics in understanding pathophysiological mechanisms of the disease from which novel biomarkers could be derived. In this single-center, prospective, case-control study, urine samples were collected from seven preterm infants with early IVH (IVH group) and from 11 preterm ones without IVH (control group) on days 1, 3 and 9 of life. Urine metabolites were evaluated using targeted liquid chromatography-tandem mass spectrometry. Demographic and perinatal-clinical characteristics were recorded. Univariate and multivariate statistical analyses were performed. Orthogonal Partial Least Squares-Discriminant Analysis showed that the study groups differed significantly due to alternation in 20 out of the 40 metabolites detected in the urine. Elevated differentiated metabolites included energy intermediates and other important compounds, whereas reduced ones various amino acids, hypoxanthine and nicotinamide. A set of metabolites showed high performance as indicators of IVH, especially during day 1. As evidenced by metabolomics, preterm neonates with IVH demonstrate significant metabolism perturbations. Potentially, a selected panel of metabolites could be used as urine biomarkers of IVH development and/or progression in high-risk preterm infants.

Quantification of 15 Psychotropic Drugs in Serum and Postmortem Blood Samples after a Modified Mini-QuEChERS by UHPLC-MS-MS.

The aim of the study was to develop a LC-MS-MS method able to detect and quantify a number of frequently prescribed antipsychotic and antidepressant drugs for toxicological purposes. Separation of compounds was performed on a C-18 RP column by Ultra High-Pressure Chromatography over a 11 min run. A modified single step QuEChERS protocol consisted essentially by the addition of acetonitrile, potassium carbonate and magnesium sulfate in 100 µL of sample, vortexing, centrifugation and evaporation has been selected. The method achieves satisfactory recoveries for 15 psychotropic drugs with a mean R% of 85% and provides efficient purification of the sample from endogenous interferences, simplicity and short sample handling times. The method was validated and provided satisfactory accuracy with recoveries ranging from 85 to 113% and precision with CV ranging from 1.2 to 13.2%. LODs were determined to be from 0.0003 to 0.017 µg/mL while LOQs were from 0.001 to 0.05 µg/mL for the 15 drugs. Matrix effect was below 20% and the analytes were stable in the matrix for 3 weeks. The method proved to be suitable for both analysis of clinical samples for Therapeutic Drug Monitoring and antemortem or postmortem whole blood samples of forensic cases. A number of samples with clinical and forensic interest were successfully analyzed demonstrating the effectiveness of QuEChERS in this field.

Hyphenated MS-based targeted approaches in metabolomics.

While global metabolic profiling (untargeted metabolomics) has been the center of much interest and research activity in the past few decades, more recently targeted metabolomics approaches have begun to gain ground. These analyses are, to an extent, more hypothesis-driven, as they focus on a set of pre-defined metabolites and aim towards their determination, often to the point of absolute quantification. The continuous development of the technological platforms used in these studies facilitates the analysis of large numbers of well-characterized metabolites present in complex matrices. The present review describes recent developments in the hyphenated chromatographic methods most often applied in targeted metabolomic/lipidomic studies (LC-MS/MS, CE-MS/MS, and GC-MS/MS), highlighting applications in the life and food/plant sciences. The review also underlines practical challenges-limitations that appear in such approaches.

Metabolic profile of human coelomic fluid.

AIM: Till now there is very limited knowledge on the molecular content of coelomic fluid and cells. This study presents the first attempt to elucidate the metabolic profile of such samples. METHODOLOGY: Samples were collected via coelocentesis from 41 women during the first trimester of gestation. Metabolic content was assessed using four different analytical platforms. For targeted analysis a hydrophilic interaction chromatography ultra high performance LC-MS/MS method was applied. Holistic analysis performed by GC-MS, NMR spectroscopy and ion cyclotron ultra-high resolution MS (FT-ICR-MS) instrumentation. RESULTS & CONCLUSIONS: Our observations suggest coelomic fluid and cells as promising biosamples, rich in metabolites with potential use in mammalian system biology studies.

Urine metabolomic profile in neonates with hypoxic-ischemic encephalopa-thy.

BACKGROUND: Metabolomics could provide valuable insights into hypoxemic-ischemic encephalopathy (HIE) revealing new disease-associated biochemical derangements. The study aimed to investigate urine metabolic changes in neonates with HIE compared to healthy controls, using targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS). PATIENTS AND METHODS: In this prospective, single-center study we enrolled neonates born at ≥ 36 weeks gestation with HIE (HIE group) and healthy controls (control group). We collected urine samples for metabolomic analysis on days one, three, and nine of life. RESULTS: Twenty-one full-term newborns were studied, 13 in the HIE group and eight in the control group. Six of the affected neonates had moderate/severe HIE and seven mild HIE. Therapeutic hypothermia was applied only in four neonates with moderate/severe HIE. Multivariate and univariate statistical analysis showed a clear separation between the HIE and the control groups. Discriminant metabolites involved pyruvic acid, amino acids, acylcarnitines, inositol, kynurenine, hippuric acid, and vitamins. CONCLUSIONS: We have identified a specific metabolic profile in neonates with HIE, adding to the existing knowledge on the disease biochemistry that may potentially help in biomarker development. HIPPOKRATIA 2017, 21(2): 80-84.

Understanding neonatal hypoxic-ischemic encephalopathy with metabolomics.

BACKGROUND:  Hypoxic-ischemic encephalopathy (HIE), a serious complication of perinatal asphyxia, is commonly associated with an unfavorable outcome. In-depth research is important not only for the interpretation of the underlying biological alternations but may also provide the basis for the development of novel diagnostic and therapeutic tools. The application of metabolomics in perinatal asphyxia/HIE is a relatively new approach. METHODS:  We performed a narrative, non-systematic review in the literature of metabolomic studies involving newborn animals and humans exposed to hypoxia-ischemia or developing perinatal asphyxia/HIE. RESULTS:  Fifteen animal studies, nine studies in human neonates, and two review articles were evaluated. Changes in the metabolomic profile of newborn animals exposed to hypoxia-ischemia and of asphyxiated neonates with HIE are presented in relation to the underlying pathophysiology. The clinical relevance of these findings is further discussed in a comprehensible to the bedside clinician manner. CONCLUSIONS:  Metabolomics may provide an explanation for the various metabolic alternations occurring in perinatal asphyxia/HIE, elucidate the biological background of the applied therapeutic interventions and promote the development of novel diagnostic-prognostic biomarkers of the disease. HIPPOKRATIA 2017, 21(3): 115-123.

A GC-MS method for the detection and quantitation of ten major drugs of abuse in human hair samples.

A sensitive analytical method has been developed in order to identify and quantify major drugs of abuse (DOA), namely morphine, codeine, 6-monoacetylmorphine, cocaine, ecgonine methyl ester, benzoylecgonine, amphetamine, methamphetamine, methylenedioxymethamphetamine and methylenedioxyamphetamine in human hair. Samples of hair were extracted with methanol under ultrasonication at 50°C after a three step rinsing process to remove external contamination and dirt hair. Derivatization with BSTFA was selected in order to increase detection sensitivity of GC/MS analysis. Optimization of derivatization parameters was based on experiments for the selection of derivatization time, temperature and volume of derivatising agent. Validation of the method included evaluation of linearity which ranged from 2 to 350ng/mg of hair mean concentration for all DOA, evaluation of sensitivity, accuracy, precision and repeatability. Limits of detection ranged from 0.05 to 0.46ng/mg of hair. The developed method was applied for the analysis of hair samples obtained from three human subjects and were found positive in cocaine, and opiates.

Multivariate analysis of chromatographic retention data as a supplementary means for grouping structurally related compounds.

In the present study a series of 45 metabolite standards belonging to four chemically similar metabolite classes (sugars, amino acids, nucleosides and nucleobases, and amines) was subjected to LC analysis on three HILIC columns under 21 different gradient conditions with the aim to explore whether the retention properties of these analytes are determined from the chemical group they belong. Two multivariate techniques, principal component analysis (PCA) and discriminant analysis (DA), were used for statistical evaluation of the chromatographic data and extraction similarities between chemically related compounds. The total variance explained by the first two principal components of PCA was found to be about 98%, whereas both statistical analyses indicated that all analytes are successfully grouped in four clusters of chemical structure based on the retention obtained in four or at least three chromatographic runs, which, however should be performed on two different HILIC columns. Moreover, leave-one-out cross-validation of the above retention data set showed that the chemical group in which an analyte belongs can be 95.6% correctly predicted when the analyte is subjected to LC analysis under the same four or three experimental conditions as the all set of analytes was run beforehand. That, in turn, may assist with disambiguation of analyte identification in complex biological extracts.

Determination of venlafaxine in post-mortem whole blood by HS-SPME and GC-NPD.

Venlafaxine is a phenethylamine derivative widely prescribed for the treatment of depression which inhibits both serotonin and norepinephrine reuptake (SNRI). In treatment with antidepressants of patient with depression and other psychiatric disorders there is also increased risk of suicidal thought and behaviour. Several lethal intoxications involving venlafaxine usually among psychotic patients have been reported in the literature. Sample preparation is of the greatest significance for a successful toxicological analysis. The development of simple, effective and rapid extraction procedures of drugs from post-mortem biological samples is a challenge. Headspace-solid phase microextraction (HS-SPME) offers significant advantages such as simplicity, low cost, compatibility with analytical systems, automation and solvent-free extraction. The aim of our work was the optimization of a HS-SPME procedure for the determination of venlafaxine in post-mortem biological samples by gas chromatography (GC) with nitrogen-phosphorous detection (NPD). Venlafaxine was extracted on 100 µm Polydimethylsiloxone Coating-Red (PDMS) SPME fiber and determined by GC-NPD. Salt addition, extraction temperature, preheating and extraction time were optimized to enhance the recovery of the extraction from aqueous solution spiked with venlafaxine. Finally the developed procedure was applied to post-mortem biological samples of a fatally poisoned woman by venlafaxine. The drug was quantified in post-mortem blood gastric and oesophagus contents of the deceased woman. A simple and rapid procedure using HS-SPME was developed for sample preparation of venlafaxine in post-mortem biological samples prior to GC-NPD determination. Validation data was satisfactory, thus enabling application in the toxicological analysis of forensic samples.

Extraction methods for the removal of phospholipids and other endogenous material from a biological fluid.

BACKGROUND: A comparison of three different sample preparation techniques for the analysis of plasma samples has been investigated to highlight the effect that these approaches have on the removal of endogenous material. The three techniques under investigation are: SPE, support assisted liquid-liquid extraction and nonspecific solvent-based protein precipitation. RESULTS: Comparisons are made on the practicalities of each approach and to allow a semiquantitative assessment between the effectiveness of these different techniques the relative amounts of phospholipids present within the sample are analyzed. Total ion chromatograms are also obtained to further study the effects of different extraction techniques in the removal of endogenous components from a biological matrix. Both of these approaches provide a very coarse measure of the cleanliness of the extracts and demonstrate that support assisted liquid-liquid extraction and an optimized SPE approach remove a greater amount of endogenous material. CONCLUSION: This study highlights the importance of sample preparation in removing endogenous material, which may have a detrimental effect on the performance of a bioanalytical assay.

Daptomycin determination by liquid chromatography-mass spectrometry in peritoneal fluid, blood plasma, and urine of clinical patients receiving peritoneal dialysis treatment.

A 13-min LC-MS method was developed for the determination of daptomycin, a new potent antibiotic, in peritoneal fluid, blood plasma, and urine of patients receiving renal replacement therapy. Chromatography was performed on a C(18) column and detection was performed by a single-quadrupole mass spectrometer coupled to LC via an electrospray interface (ESI). The column effluent was also monitored at 370 nm using a photodiode-array detector. The developed method provided a linear dynamic range for concentrations from 0.5 microg mL(-1) to 100 microg mL(-1). Method precision and accuracy were found to be satisfactory for clinical application, thus the method was successfully used for the analysis of daptomycin in pharmacokinetic studies. The drug was preventively administered against Gram-positive infections to 19 clinical patients undergoing peritoneal dialysis. Peritoneal fluid, blood plasma, and urine samples were collected at 13 time points over a period of 48 h. Clinical samples were analysed following simple sample-preparation procedures and daptomycin was unambiguously detected and quantified.

Solid phase microextraction applied to the analysis of organophosphorus insecticides in fruits.

Trace amounts of organophosphorus pesticides (OPs) were determined in various fruits by headspace solid phase microextraction (HS-SPME) and gas chromatography-nitrogen phosphorous detection (GC-NPD). Sampling from the headspace enhanced method selectivity, whereas at the same time improved fiber life time and method sensitivity. Diazinon, parathion, methyl parathion, malathion and fenithrothion were determined in various fruits: more than 150 samples of 21 types of fruits were studied. SPME-GC-NPD provided a useful and very efficient analytical tool: method linearity ranged from 1.2 to 700 ng/ml. Limits of detection (LODs) and quantitation (LOQs) ranged from 0.03 to 3 ng/ml and 0.12 to 10 ng/ml respectively, values well below the residue limits set by the EU. Less than 2% of the samples were found positive containing amounts higher than the EU limits. The effect of fruit peeling and washing was also investigated.

Headspace solid phase microextraction for the gas chromatographic analysis of methyl-parathion in post-mortem human samples. Application in a suicide case by intravenous injection.

A simple and rapid procedure for the determination of methyl-parathion (m-p) in post-mortem biological samples was developed using headspace solid phase microextraction (SPME) and gas chromatography (GC) with nitrogen-phosphorous detection (NPD). Methyl-parathion was extracted on 85 microm polyacrylate SPME fiber. Salt addition, extraction temperature, and extraction time were optimized to enhance the sensitivity of the method. The linearity (y = 0.0473x - 0.0113, R2 = 0.9992) and the dynamic range (0.1-40 microg/ml) were found very satisfactory. The recoveries of methyl-parathion were found to be 46% in spiked human whole blood, 53% in spiked homogenized liver tissue, and 54% in spiked homogenized kidney tissue compared with samples prepared in water. The coefficients of variations for 2, 4, and 20 microg/ml of methyl-parathion in blood ranged from 0.9 to 5.1%, whereas the detection limit of the method was satisfactory (1 ng/ml in aqueous samples, 50 ng/ml in whole blood). The developed procedure was applied to post-mortem biological samples from a 21-year-old woman fatally poisoned (suicide) by intravenous injection of methyl-parathion. The intact insecticide was found in the post-mortem blood at a concentration of 24 microg/ml. No methyl-parathion was detected in the liver, kidneys, and gastric contents.

Selective solid-phase extraction sorbent for caffeine made by molecular imprinting.

A molecularly imprinted polymer (MIP) was prepared with caffeine as the template molecule. Thermal polymerisation (60 degrees C) was optimised, varying ratios of monomer, cross linker and template. The polymer was used as a solid-phase extraction (SPE) sorbent, for selective trapping and pre-concentration of caffeine. Caffeine was loaded on the MIP-SPE cartridge using different loading conditions (solvents, pH value). Washing and elution of the caffeine bound to the MIP was studied utilising different protocols. The extraction protocol was successfully applied to the direct extraction of caffeine from beverages and spiked human plasma.

Immunoaffinity chromatography for the sample pretreatment of Taxus plant and cell extracts prior to analysis of taxanes by high-performance liquid chromatography.

The application of immunoaffinity chromatography for the purification of Taxus plant and cell extracts prior to the HPLC analysis is described. Polyclonal antibodies raised against 10-deacetylbaccatin III (10-DAB III), paclitaxel's main precursor in plant, were characterised by enzymed-linked immunosorbent assay. Immunoglobulins from selected antisera were immobilised on CNBr-activated Sepharose 4B. The immunoaffinity column was used for the purification of plant and plant cell culture extracts prior to their analysis by HPLC. Immunoaffinity chromatography enabled the selective concentration of taxoids and enhanced sample clean-up.

On selection mechanisms during initial evolution and on the possible role of ionic balance.

Initial evolution at the molecular level can proceed through mechanisms that enhance either the generation or the survival of certain molecules. Phenomena related to ionic balance can be the basis for both generative and survival selection mechanisms that may have driven the initial evolution of macromolecules. An important advantage of mechanisms based on ionic balance phenomena is that they can conceivably generate spatial and temporal inhomogeneities in semi-enclosed spaces within cavities of porous materials and/or membranes. Under certain circumstances, such inhomogeneities are required for initial evolution to proceed.

Solid-phase microextraction for the analysis of biological samples.

Solid-phase microextraction (SPME) has been introduced for the extraction of organic compounds from environmental samples. This relatively new extraction technique has now also gained a lot of interest in a broad field of analysis including food, biological and pharmaceutical samples. SPME has a number of advantages such as simplicity, low cost, compatibility with analytical systems, automation and the solvent-free extraction. The last few years, SPME has been combined with liquid chromatography and capillary electrophoresis, besides the generally used coupling to gas chromatography, and has been applied to various biological samples such as, e.g., urine, plasma and hair. The objective of the present paper is a survey of the application of SPME for the analysis of biological samples. Papers about the analysis of biologically active compounds are categorised and reviewed. The impact of SPME on various analytical fields (toxicological, forensic, clinical, biochemical, pharmaceutical, and natural products) is illustrated. The main features of SPME and its modes are briefly described and important aspects about its application for the determination of pharmaceuticals, drugs of abuse and compounds of clinical and toxicological interest are discussed. SPME is compared with other sample pretreatment techniques. The potential of SPME and its main advantages are demonstrated. Special attention is paid to new trends in applications of SPME in bioanalysis.