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Article ; Online: Longitudinal Plant Health Monitoring via High-Resolution Mass Spectrometry Screening Workflows

Anthi Panara / Evagelos Gikas / Anastasia Koupa / Nikolaos S. Thomaidis

Molecules, Vol 28, Iss 6771, p

Application to a Fertilizer Mediated Tomato Growth Experiment

2023 Volume 6771

Abstract: Significant efforts have been spent in the modern era towards implementing environmentally friendly procedures like composting to mitigate the negative effects of intensive agricultural practices. In this context, a novel fertilizer was produced via the ... ...

Abstract	Significant efforts have been spent in the modern era towards implementing environmentally friendly procedures like composting to mitigate the negative effects of intensive agricultural practices. In this context, a novel fertilizer was produced via the hydrolysis of an onion-derived compost, and has been previously comprehensively chemically characterized. In order to characterize its efficacy, the product was applied to tomato plants at five time points to monitor plant health and growth. Control samples were also used at each time point to eliminate confounding parameters due to the plant’s normal growth process. After harvesting, the plant leaves were extracted using aq. MeOH (70:30, v / v ) and analyzed via UPLC-QToF-MS, using a C18 column in both ionization modes (±ESI). The data-independent (DIA/bbCID) acquisition mode was employed, and the data were analyzed by MS-DIAL. Statistical analysis, including multivariate and trend analysis for longitudinal monitoring, were employed to highlight the differentiated features among the controls and treated plants as well as the time-point sequence. Metabolites related to plant growth belonging to several chemical classes were identified, proving the efficacy of the fertilizer product. Furthermore, the efficiency of the analytical and statistical workflows utilized was demonstrated.
Keywords	onion-based fertilizer ; tomato leaves ; plant growth ; HRMS ; time series ; chemometrics ; Organic chemistry ; QD241-441
Subject code	580
Language	English
Publishing date	2023-09-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Comprehensive HRMS Chemical Characterization of Pomegranate-Based Antioxidant Drinks via a Newly Developed Suspect and Target Screening Workflow

Anthi Panara / Evagelos Gikas / Ilias Tzavellas / Nikolaos S. Thomaidis

Molecules, Vol 28, Iss 4986, p

2023 Volume 4986

Abstract: Antioxidants play a significant role in human health, protecting against a variety of diseases. Therefore, the development of products with antioxidant activity is becoming increasingly prominent in the human lifestyle. New antioxidant drinks containing ... ...

Abstract	Antioxidants play a significant role in human health, protecting against a variety of diseases. Therefore, the development of products with antioxidant activity is becoming increasingly prominent in the human lifestyle. New antioxidant drinks containing different percentages of pomegranate, blackberries, red grapes, and aronia have been designed, developed, and manufactured by a local industry. The comprehensive characterization of the drinks’ constituents has been deemed necessary to evaluate their bioactivity. Thus, LC-qTOFMS has been selected, due to its sensitivity and structure identification capability. Both data-dependent and -independent acquisition modes have been utilized. The data have been treated according to a novel, newly designed workflow based on MS-DIAL and MZmine for suspect, as well as target screening. The classical MS-DIAL workflow has been modified to perform suspect and target screening in an automatic way. Furthermore, a novel methodology based on a compiled bioactivity-driven suspect list was developed and expanded with combinatorial enumeration to include metabolism products of the highlighted metabolites. Compounds belonging to ontologies with possible antioxidant capacity have been identified, such as flavonoids, amino acids, and fatty acids, which could be beneficial to human health, revealing the importance of the produced drinks as well as the efficacy of the new in-house developed workflow.
Keywords	antioxidant drinks ; novel workflows ; HRMS ; pomegranate ; suspect screening methodology ; Organic chemistry ; QD241-441
Subject code	540
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: From By-Products to Fertilizer

Anthi Panara / Evagelos Gikas / Nikolaos S. Thomaidis

Molecules, Vol 27, Iss 3498, p

Chemical Characterization Using UPLC-QToF-MS via Suspect and Non-Target Screening Strategies

2022 Volume 3498

Abstract: The increasing demands of agriculture and the food market have resulted in intensive agricultural practices using synthetic fertilizers to maximize production. However, significant efforts have been made to implement more environmentally friendly ... ...

Abstract	The increasing demands of agriculture and the food market have resulted in intensive agricultural practices using synthetic fertilizers to maximize production. However, significant efforts have been made to implement more environmentally friendly procedures, such as composting, to overcome the adverse impact of these invasive practices. In the terms of this research, composting was applied to the production of two biofertilizers, using onion and mushroom by-products as raw materials respectively. The main purposes of this work were to identify the compounds that pass from the raw materials to the final products (onion-based and mushroom-based), as well as the characterization of the chemical profile of these final products following suspect and non-target screening workflows via UPLC-qToF-MS. Overall, 14 common compounds were identified in the onion and its final product, while 12 compounds were found in the mushroom and its corresponding product. These compounds belong to fatty acids, organic acids, and flavonoids, which could be beneficial to plant health. The determination of parameters, such as the pH, conductivity, organic matter, nitrogen content, and elemental analysis, were conducted for the overall characterization of the aforementioned products.
Keywords	onion ; mushroom ; fertilizer ; UPLC-QToF-MS ; suspect screening ; non-target screening ; Organic chemistry ; QD241-441
Subject code	540
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A Novel Validated Injectable Colistimethate Sodium Analysis Combining Advanced Chemometrics and Design of Experiments

Ioanna Dagla / Anthony Tsarbopoulos / Evagelos Gikas

Molecules, Vol 26, Iss 1546, p

2021 Volume 1546

Abstract: Colistimethate sodium (CMS) is widely administrated for the treatment of life-threatening infections caused by multidrug-resistant Gram-negative bacteria. Until now, the quality control of CMS formulations has been based on microbiological assays. Herein, ...

Abstract	Colistimethate sodium (CMS) is widely administrated for the treatment of life-threatening infections caused by multidrug-resistant Gram-negative bacteria. Until now, the quality control of CMS formulations has been based on microbiological assays. Herein, an ultra-high-performance liquid chromatography coupled to ultraviolet detector methodology was developed for the quantitation of CMS in injectable formulations. The design of experiments was performed for the optimization of the chromatographic parameters. The chromatographic separation was achieved using a Waters Acquity BEH C 8 column employing gradient elution with a mobile phase consisting of (A) 0.001 M aq. ammonium formate and (B) methanol/acetonitrile 79/21 ( v / v ). CMS compounds were detected at 214 nm. In all, 23 univariate linear-regression models were constructed to measure CMS compounds separately, and one partial least-square regression (PLSr) model constructed to assess the total CMS amount in formulations. The method was validated over the range 100–220 μg mL −1 . The developed methodology was employed to analyze several batches of CMS injectable formulations that were also compared against a reference batch employing a Principal Component Analysis, similarity and distance measures, heatmaps and the structural similarity index. The methodology was based on freely available software in order to be readily available for the pharmaceutical industry.
Keywords	colistimethate ; UPLC–UV ; multivariate analysis ; pharmaceutical formulations ; quality control ; partial least square regression ; Organic chemistry ; QD241-441
Subject code	621
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Colistimethate Acidic Hydrolysis Revisited

Ioanna Dagla / Anthony Tsarbopoulos / Evagelos Gikas

Molecules, Vol 26, Iss 2, p

Arrhenius Equation Modeling Using UPLC-QToF MS

2021 Volume 447

Abstract: Colistimethate (CMS), the prodrug of polymyxin E (colistin), is an antibiotic widely used as a last-line therapy against multidrug resistant Gram-negative bacteria, but little is known about its pharmacokinetics as its administration has stopped as a ... ...

Abstract	Colistimethate (CMS), the prodrug of polymyxin E (colistin), is an antibiotic widely used as a last-line therapy against multidrug resistant Gram-negative bacteria, but little is known about its pharmacokinetics as its administration has stopped as a result of high neuro- and nephro-toxicity. The measurement of CMS levels in patients’ biological fluids is of great importance in order to find the optimal dose regimen reducing the drug toxicity. Until now, CMS assay methods are based on the indirect determination after its hydrolysis to colistin (CS). Herein, the aim is to find the optimal conditions for the complete hydrolysis of CMS to CS. The reaction was studied at accelerated conditions: 40 °C, 50 °C, and 60 °C, and the results were evaluated by assessing the Arrhenius equation and computation employing the Tenua software. A validated analytical methodology based on ultra-performance liquid chromatography (UPLC) coupled to a hybrid quadrupole time of flight (QToF) instrument is developed for the simultaneous measurement of CMS and CS. The current methodology resulted in complete hydrolysis, in contrast with the previously reported one.
Keywords	colistimethate ; stability ; Arrhenius ; assay ; LC-MS ; Organic chemistry ; QD241-441
Subject code	621
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Integrated HPTLCâbased Methodology for the Tracing of Bioactive Compounds in Herbal Extracts Employing Multivariate Chemometrics. A Case Study on Morus alba

Chaita, Eliza / Evagelos Gikas / Nektarios Aligiannis

Phytochemical analysis. 2017 Mar., v. 28, no. 2

2017

Abstract: INTRODUCTION: In drug discovery, bioassayâguided isolation is a wellâestablished procedure, and still the basic approach for the discovery of natural products with desired biological properties. However, in these procedures, the most laborious and ... ...

Abstract	INTRODUCTION: In drug discovery, bioassayâguided isolation is a wellâestablished procedure, and still the basic approach for the discovery of natural products with desired biological properties. However, in these procedures, the most laborious and timeâconsuming step is the isolation of the bioactive constituents. A prior identification of the compounds that contribute to the demonstrated activity of the fractions would enable the selection of proper chromatographic techniques and lead to targeted isolation. OBJECTIVE: The development of an integrated HPTLCâbased methodology for the rapid tracing of the bioactive compounds during bioassayâguided processes, using multivariate statistics. Materials and Methods â The methanol extract of Morus alba was fractionated employing CPC. Subsequently, fractions were assayed for tyrosinase inhibition and analyzed with HPTLC. PLSâR algorithm was performed in order to correlate the analytical data with the biological response of the fractions and identify the compounds with the highest contribution. Two methodologies were developed for the generation of the dataset; one based on manual peak picking and the second based on chromatogram binning. Results and Discussion â Both methodologies afforded comparable results and were able to trace the bioactive constituents (e.g. oxyresveratrol, transâdihydromorin, 2,4,3â²âtrihydroxydihydrostilbene). The suggested compounds were compared in terms of Rf values and UV spectra with compounds isolated from M. alba using typical bioassayâguided process. CONCLUSION: Chemometric tools supported the development of a novel HPTLCâbased methodology for the tracing of tyrosinase inhibitors in M. alba extract. All steps of the experimental procedure implemented techniques that afford essential key elements for application in highâthroughput screening procedures for drug discovery purposes. Copyright Â© 2017 John Wiley & Sons, Ltd.
Keywords	Morus alba ; algorithms ; bioactive compounds ; case studies ; chemometrics ; chromatography ; data collection ; drugs ; methanol ; multivariate analysis ; screening
Language	English
Dates of publication	2017-03
Size	p. 125-131.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	1073576-8
ISSN	1099-1565 ; 0958-0344
ISSN (online)	1099-1565
ISSN	0958-0344
DOI	10.1002/pca.2670
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Plasma Metabolomic Alterations Induced by COVID-19 Vaccination Reveal Putative Biomarkers Reflecting the Immune Response

Ioanna Dagla / Aikaterini Iliou / Dimitra Benaki / Evagelos Gikas / Emmanuel Mikros / Tina Bagratuni / Efstathios Kastritis / Meletios A. Dimopoulos / Evangelos Terpos / Anthony Tsarbopoulos

Cells, Vol 11, Iss 1241, p

2022 Volume 1241

Abstract: Vaccination is currently the most effective strategy for the mitigation of the COVID-19 pandemic. mRNA vaccines trigger the immune system to produce neutralizing antibodies (NAbs) against SARS-CoV-2 spike proteins. However, the underlying molecular ... ...

Abstract	Vaccination is currently the most effective strategy for the mitigation of the COVID-19 pandemic. mRNA vaccines trigger the immune system to produce neutralizing antibodies (NAbs) against SARS-CoV-2 spike proteins. However, the underlying molecular processes affecting immune response after vaccination remain poorly understood, while there is significant heterogeneity in the immune response among individuals. Metabolomics have often been used to provide a deeper understanding of immune cell responses, but in the context of COVID-19 vaccination such data are scarce. Mass spectrometry (LC-MS) and nuclear magnetic resonance (NMR)-based metabolomics were used to provide insights based on the baseline metabolic profile and metabolic alterations induced after mRNA vaccination in paired blood plasma samples collected and analysed before the first and second vaccination and at 3 months post first dose. Based on the level of NAbs just before the second dose, two groups, “low” and “high” responders, were defined. Distinct plasma metabolic profiles were observed in relation to the level of immune response, highlighting the role of amino acid metabolism and the lipid profile as predictive markers of response to vaccination. Furthermore, levels of plasma ceramides along with certain amino acids could emerge as predictive biomarkers of response and severity of inflammation.
Keywords	COVID-19 ; metabolomics ; neutralizing antibodies (NAbs) ; NMR ; LC-MS ; ceramides ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Post-acquisition spectral stitching. An alternative approach for data processing in untargeted metabolomics by UHPLC-ESI(−)-HRMS

Baira, Eirini / Alexios-Leandros Skaltsounis / Deligeorgis Stelios G / Eleni Siapi / Evagelos Gikas / Panagiotis Zoumpoulakis

Journal of chromatography. 2017 Mar. 15, v. 1047

2017

Abstract: In the case of the MS-based metabolomics, the large number of false positives remains a fundamental issue.The aim of this study was to develop a new strategy, which highlights the number of the reliable features i.e. the detected features that correspond ...

Abstract	In the case of the MS-based metabolomics, the large number of false positives remains a fundamental issue.The aim of this study was to develop a new strategy, which highlights the number of the reliable features i.e. the detected features that correspond to a consistent peak according to chromatographic and mass spectrometric criteria.For the analysis blood samples from 20 chickens, which were administrated with naringin and 9 samples from control, were analyzed by UHPLC-HRMS (Orbitrap Velos). Two methodologies have been compared for data processing. In the first one (classical approach), all data in the 100–900 m/z mass-to charge range were included for the data processing procedure whereas for the newly developed methodology, the data were shred in 100Da slices generating 8 datasets, which have been then subjected to the downstream MS data processing. Each dataset was treated separately and the m/z_tR features obtained by either VIP’s or t-test values were merged and used as the input for the construction of the general model.The new methodology resulted to a 4-fold increase of the peaks that could be considered chromatographically and mass spectrometrically valid.A new strategy was reported on the detection of chromatographically reliable features during a metabolomic approach. The shredding of the LC–MS chromatograms into multiple m/z ranges increased the number of the identified chromatographically reliable features.
Keywords	blood sampling ; chickens ; data collection ; hematologic tests ; liquid chromatography ; mass spectrometry ; metabolomics ; naringin ; t-test
Language	English
Dates of publication	2017-0315
Size	p. 106-114.
Publishing place	Elsevier B.V.
Document type	Article
ISSN	1570-0232
DOI	10.1016/j.jchromb.2016.10.030
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Human Melanoma-Cell Metabolic Profiling

Mariangela Kosmopoulou / Aikaterini F. Giannopoulou / Aikaterini Iliou / Dimitra Benaki / Aristeidis Panagiotakis / Athanassios D. Velentzas / Eumorphia G. Konstantakou / Issidora S. Papassideri / Emmanuel Mikros / Dimitrios J. Stravopodis / Evagelos Gikas

International Journal of Molecular Sciences, Vol 21, Iss 2436, p

Identification of Novel Biomarkers Indicating Metastasis

2020 Volume 2436

Abstract: Melanoma is the most aggressive type of skin cancer, leading to metabolic rewiring and enhancement of metastatic transformation. Efforts to improve its early and accurate diagnosis are largely based on preclinical models and especially cell lines. Hence, ...

Abstract	Melanoma is the most aggressive type of skin cancer, leading to metabolic rewiring and enhancement of metastatic transformation. Efforts to improve its early and accurate diagnosis are largely based on preclinical models and especially cell lines. Hence, we herein present a combinational Nuclear Magnetic Resonance (NMR)- and Ultra High Performance Liquid Chromatography-High-Resolution Tandem Mass Spectrometry (UHPLC-HRMS/MS)-mediated untargeted metabolomic profiling of melanoma cells, to landscape metabolic alterations likely controlling metastasis. The cell lines WM115 and WM2664, which belong to the same patient, were examined, with WM115 being derived from a primary, pre-metastatic, tumor and WM2664 clonally expanded from lymph-node metastases. Metabolite samples were analyzed using NMR and UHPLC-HRMS. Multivariate statistical analysis of high resolution NMR and MS (positive and negative ionization) results was performed by Principal Component Analysis (PCA), Partial Least Squares-Discriminant Analysis (PLS-DA) and Orthogonal Partial Least Squares-Discriminant Analysis (OPLS-DA), while metastasis-related biomarkers were determined on the basis of VIP lists, S-plots and Student’s t-tests. Receiver Operating Characteristic (ROC) curves of NMR and MS data revealed significantly differentiated metabolite profiles for each cell line, with WM115 being mainly characterized by upregulated levels of phosphocholine, choline, guanosine and inosine. Interestingly, WM2664 showed notably increased contents of hypoxanthine, myo-inositol, glutamic acid, organic acids, purines, pyrimidines, AMP, ADP, ATP and UDP(s), thus indicating the critical roles of purine, pyrimidine and amino acid metabolism during human melanoma metastasis.
Keywords	biomarker ; cancer ; melanoma ; metabolomics ; metastasis ; MS ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	572
Language	English
Publishing date	2020-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Development and validation of a combined methodology for assessing the total quality control of herbal medicinal products--application to oleuropein preparations.

Nikolaos Lemonakis / Evagelos Gikas / Maria Halabalaki / Alexios-Leandros Skaltsounis

PLoS ONE, Vol 8, Iss 10, p e

2013 Volume 78277

Abstract: Oleuropein (OE) is a secoiridoid glycoside, which occurs mostly in the Oleaceae family presenting several pharmacological properties, including antioxidant, cardio-protective, anti-atherogenic effects etc. Based on these findings OE is commercially ... ...

Abstract	Oleuropein (OE) is a secoiridoid glycoside, which occurs mostly in the Oleaceae family presenting several pharmacological properties, including antioxidant, cardio-protective, anti-atherogenic effects etc. Based on these findings OE is commercially available, as Herbal Medicinal Product (HMP), claimed for its antioxidant effects. As there are general provisions of the medicine regulating bodies e.g. European Medicines Agency, the quality of the HMP's must always be demonstrated. Therefore, a novel LC-MS methodology was developed and validated for the simultaneous quantification of OE and its main degradation product, hydroxytyrosol (HT), for the relevant OE claimed HMP's. The internal standard (IS) methodology was employed and separation of OE, HT and IS was achieved on a C18 Fused Core column with 3.1 min overall run time employing the SIM method for the analytical signal acquisition. The method was validated according to the International Conference on Harmonisation requirements and the results show adequate linearity (r(2) > 0.99) over a wide concentration range [0.1-15 μg/mL (n=12)] and a LLOQ value of 0.1 μg/mL, for both OE and HT. Furthermore, as it would be beneficial to control the quality taking into account all the substances of the OE claimed HMP's; a metabolomics-like approach has been developed and applied for the total quality control of the different preparations employing UHPLC-HRMS-multivariate analysis (MVA). Four OE-claimed commercial HMP's have been randomly selected and MVA similarity-based measurements were performed. The results showed that the examined samples could also be differentiated as evidenced according to their scores plot. Batch to batch reproducibility between the samples of the same brand has also been determined and found to be acceptable. Overall, the developed combined methodology has been found to be an efficient tool for the monitoring of the HMP's total quality. Only one OE HMP has been found to be consistent to its label claim.
Keywords	Medicine ; R ; Science ; Q
Subject code	600
Language	English
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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