Aroma determination in alcoholic beverages: Green MS-based sample preparation approaches.

Aroma determination in alcoholic beverages has become a hot research topic due to the ongoing effort to obtain quality products, especially in a globalized market. Consumer satisfaction is mainly achieved by balancing several aroma compounds, which are mixtures of numerous volatile molecules enclosed in challenging matrices. Thus, sample preparation strategies for quality control and product development are required. They involve several steps including copious amounts of hazardous solvents or time-consuming procedures. This is bucking the trend of the ever-increasing pressure to reduce the environmental impact of analytical chemistry processes. Hence, the evolution of sample preparation procedures has directed towards miniaturized techniques to decrease or avoid the use of hazardous solvents and integrating sampling, extraction, and enrichment of the targeted analytes in fewer steps. Mass spectrometry coupled to gas or liquid chromatography is particularly well suited to address the complexity of these matrices. This review surveys advancements of green miniaturized techniques coupled to mass spectrometry applied on all categories of odor-active molecules in the most consumed alcoholic beverages: beer, wine, and spirits. The targeted literature consider progresses over the past 20 years.

Cytotoxic Compounds from Alcyoniidae: An Overview of the Last 30 Years.

The octocoral family Alcyoniidae represents a rich source of bioactive substances with intriguing and unique structural features. This review aims to provide an updated overview of the compounds isolated from Alcyoniidae and displaying potential cytotoxic activity. In order to allow a better comparison among the bioactive compounds, we focused on molecules evaluated in vitro by using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay, by far the most widely used method to analyze cell proliferation and viability. Specifically, we surveyed the last thirty years of research, finding 153 papers reporting on 344 compounds with proven cytotoxicity. The data were organized in tables to provide a ranking of the most active compounds, to be exploited for the selection of the most promising candidates for further screening and pre-clinical evaluation as anti-cancer agents. Specifically, we found that (22S,24S)-24-methyl-22,25-epoxyfurost-5-ene-3ß,20ß-diol (16), 3ß,11-dihydroxy-24-methylene-9,11-secocholestan-5-en-9-one (23), (24S)-ergostane-3ß,5α,6ß,25 tetraol (146), sinulerectadione (227), sinulerectol C (229), and cladieunicellin I (277) exhibited stronger cytotoxicity than their respective positive control and that their mechanism of action has not yet been further investigated.

Multi-Task Neural Networks and Molecular Fingerprints to Enhance Compound Identification from LC-MS/MS Data.

Mass spectrometry (MS) is widely used for the identification of chemical compounds by matching the experimentally acquired mass spectrum against a database of reference spectra. However, this approach suffers from a limited coverage of the existing databases causing a failure in the identification of a compound not present in the database. Among the computational approaches for mining metabolite structures based on MS data, one option is to predict molecular fingerprints from the mass spectra by means of chemometric strategies and then use them to screen compound libraries. This can be carried out by calibrating multi-task artificial neural networks from large datasets of mass spectra, used as inputs, and molecular fingerprints as outputs. In this study, we prepared a large LC-MS/MS dataset from an on-line open repository. These data were used to train and evaluate deep-learning-based approaches to predict molecular fingerprints and retrieve the structure of unknown compounds from their LC-MS/MS spectra. Effects of data sparseness and the impact of different strategies of data curing and dimensionality reduction on the output accuracy have been evaluated. Moreover, extensive diagnostics have been carried out to evaluate modelling advantages and drawbacks as a function of the explored chemical space.

From the Streets to the Judicial Evidence: Determination of Traditional Illicit Substances in Drug Seizures by a Rapid and Sensitive UHPLC-MS/MS-Based Platform.

According to the 2021 World Drug Report, around 275 million people use drugs of abuse, and 36 million people suffer from addiction, fostering a thriving market for illicit substances. In Italy, 30,083 people were reported to the Judicial Authority for offenses in violation of the Italian Law D.P.R. 309/1990. These offences are sentenced after a qualitative-quantitative analysis of seized materials. Given the large quantity of seized drugs and the need to perform accurate analytical determinations, Italian forensic laboratories struggle to complete analyses in a short time, delaying the entire reporting process needed to achieve sentencing. For this purpose, an UHPLC-MS/MS-based platform was developed at the University of Milano-Bicocca to support law-enforcement authorities. Software was designed to easily manage street seizure acquisition, documentation registration, and sampling. A sensitive UHPLC-MS/MS method was fully validated for the quantification of the traditional illicit substances (cocaine, heroin, 6-MAM, morphine, amphetamine, methamphetamine, MDMA, ketamine, GHB, GBL, LSD, trans-∆9-THC, and THCA) at the ppb level. The final report is relayed to the Prefecture in 3-4 days, even within 24 h for urgent requests. The platform allows for semi-automatic data handling to minimize erroneous results for an accurate report generation by standardized procedures.

Parsimonious Optimization of Multitask Neural Network Hyperparameters.

Neural networks are rapidly gaining popularity in chemical modeling and Quantitative Structure-Activity Relationship (QSAR) thanks to their ability to handle multitask problems. However, outcomes of neural networks depend on the tuning of several hyperparameters, whose small variations can often strongly affect their performance. Hence, optimization is a fundamental step in training neural networks although, in many cases, it can be very expensive from a computational point of view. In this study, we compared four of the most widely used approaches for tuning hyperparameters, namely, grid search, random search, tree-structured Parzen estimator, and genetic algorithms on three multitask QSAR datasets. We mainly focused on parsimonious optimization and thus not only on the performance of neural networks, but also the computational time that was taken into account. Furthermore, since the optimization approaches do not directly provide information about the influence of hyperparameters, we applied experimental design strategies to determine their effects on the neural network performance. We found that genetic algorithms, tree-structured Parzen estimator, and random search require on average 0.08% of the hours required by grid search; in addition, tree-structured Parzen estimator and genetic algorithms provide better results than random search.

Proteomic approaches to decipher cancer cell secretome.

In this review, we give an overview of the actual proteomic approaches used in the study of cancer cells secretome. In particular, we describe the proteomic strategies to decipher cancer cell secretome initially focusing on the different aspects of sample preparation. We examine the issues related to the presence of low abundant proteins, the analysis of secreted proteins in the conditioned media with or without the removal of fetal bovine serum and strategies developed to reduce intracellular protein contamination. As regards the identification and quantification of secreted proteins, we described the different proteomic approaches used, i.e. gel-based, MS-based (label-based and label-free), and the antibody and array-based methods, together with some of the most recent applications in the field of cancer research. Moreover, we describe the bioinformatics tools developed for the in silico validation and characterization of cancer cells secretome. We also discuss the most important available tools for protein annotation and for prediction of classical and non-classical secreted proteins. In summary in this review advances, concerns and challenges in the field of cancer secretome analysis are discussed.

It's Only a Part of the Story: Analytical Investigation of the Inks and Dyes Used in the Privilegium Maius.

The Privilegium maius is one of the most famous and spectacular forgeries in medieval Europe. It is a set of charters made in the 14th century upon commitment by Duke Rudolf IV, a member of the Habsburg family, to elevate the rank and the prestige of his family. These five charters, now kept at the Österreichisches Staatsarchiv in Vienna, have been subjected to a thorough interdisciplinary study in order to shed light on its controversial story. The charters are composed of pergamenaceous documents bound to wax seals with coloured textile threads. The present contribution concerns the characterisation of the inks used for writing and of the dyes used to colour to the threads: Are they compatible with the presumed age of the charters? Though showing only a part of the whole story of the charters, dyes analysis could contribute in assessing their complex history from manufacturing to nowadays. The dyes were characterised with non-invasive in situ measurements by means of fibre optic (FORS) and with micro-invasive measurements by means of Surface Enhanced Raman Spectroscopy (SERS) and High-Performance Liquid Chromatography with Mass Spectrometry (HPLC-MS) analysis. The results showed that the threads of four of the charters (three dyed with madder, one with orchil) were apparently coloured at different dyeing stages, then re-dyed in the 19-20th century.

Method for Noninvasive Analysis of Proteins and Small Molecules from Ancient Objects.

Proteins and small molecules from ancient objects and cultural heritage can provide key information and contribute to study the context of objects and artists. However, all present-day protocols and strategies for the analysis of ancient samples are often invasive and require microsampling. Here, we present a new method for the noninvasive analysis of proteins and small molecules: the technique uses a special ethyl-vinyl acetate film functionalized with strong cation/anion exchange and C8 resins, for interacting with both proteins and small molecules present on the surface of the objects, followed by LC-MS/MS analysis. The new method was fully validated for the determination of both proteins and small molecules on several types of supports, showing excellent analytical performances such as, for example, R2 of the calibration curve of 0.98 and 0.99 for proteins and small molecules, low but very repeatable recoveries, particularly adequate for investigations on precious ancient samples that must not be altered by the analytical procedure. ESEM images and LED multispectral imaging confirmed that no damages or alterations occurred onto the support surfaces and no residues were left from the extractive film. Finally, the new method was applied for the characterization of the binders of a historical fresco of the XVI century from the Flemish painter Paul Brill and of a recently discovered fresco from Isidoro Bianchi (XVII century). Moreover the method was employed for the identification of the colorant used by Pietro Gallo (XIV century) on a wood panel. The method here reported can be easily applied to any other research on ancient precious objects and cultural heritage, since it does not require microsampling and the proteins/small molecules extraction can be performed directly in situ, leaving the object unchanged and intact.

IEF peptide fractionation method combined to shotgun proteomics enhances the exploration of rice milk proteome.

We conducted a proteomics study in order to detect the proteomic method which provides the most complete characterization of the proteins of rice milk. In particular, we compared the results obtained from LC-MS/MS after protein precipitation with acetone or TCA, as well as the results obtained from LC-MS/MS after protein prefractionation based on SDS-PAGE (GeLC-MS/MS) or ProteoMiner™ technology (ProteoMiner-LC-MS/MS), and after peptide prefractionation based on IEF (pIEF-LC-MS/MS). A total of 158 protein species have been detect in rice milk. The physical-chemical analysis and classification of the identified proteins were also reported. In particular, we showed that pIEF-LC-MS/MS method led to a significant increase in the proteome coverage, allowing the identification of a total of 96 proteins of milk rice. This study demonstrates the utility of a prefractionation step based on pIEF before the shotgun proteomic analysis and offers an in-depth insight into the rice milk proteome.

A metaproteomic approach dissecting major bacterial functions in the rhizosphere of plants living in serpentine soil.

A metaproteomic approach, based on liquid chromatography-high resolution mass spectrometry (LC-HRMS) analysis, was followed to map the major bacterial metabolic functions associated with the rhizosphere of metal-tolerant and metal hyperaccumulator plants, growing in a serpentine soil naturally contaminated by heavy metals such as Ni, Co and Cr. In particular, an "in-house" bacterial protein database was built based on the genera recognised by 16S rDNA profiling, then it was used for protein identification from LC-MS data. The combination of the information arising from three different extraction protocols, applied to each soil sample, permitted the identification of almost 800 proteins, corresponding to functions assigned to proper Gene Ontology categories. Mainly proteins involved in response to stimulus or in transport of metals and nutrients revealed variability of bacteria responses to microenvironment conditions. As for taxonomy, Phyllobacterium, Microbacterium oxidans, Pseudomonas oryzihabitans, Stenotrophomonas rhizophila and Bacillus methylotrophicus bacterial species were more represented in the rhizosphere samples of the metal-tolerant Biscutella laevigata and of the Ni hyperaccumulator Noccaea caerulescens with respect to bulk soil. Combining 16S rRNA gene-based sequencing and metaproteomic analysis, we get insights into microbial community functions and their interaction with plants colonising the stressful environment of serpentine soils.

HMGB1 Osteo-Modulatory Action on Osteosarcoma SaOS-2 Cell Line: An Integrated Study From Biochemical and -Omics Approaches.

High mobility group box protein-1 (HMGB1) is released from cells under various pathological conditions and it plays a pivotal role as an alarmin signaling tissue damage. Little is known about the impact of HMGB1 in bone repair and remodeling. To this aim, we focused on HMGB1-induced effects on the in vitro osteoblast model SaOS-2. Cell proliferation was stimulated with a maximum at concentration of 2.5 nM, and such a dose also stimulated cell migration and scratch wound healing. We then characterized the modulatory effect of HMGB1 on bone biology, by using osteogenesis/mineralization assays, a PCR array, and the analysis of a series of osteogenic markers. We performed also a proteomic screening using SWATH-MS on SaOS-2 cell exposed to HMGB1 and we provide evidence for proteins modulated in HMGB1 exposed cells. Taken together, our data demonstrate that SaOS-2 cell proliferation, migration, and osteogenic differentiation were increased by HMGB1. We, therefore, propose that HMGB1 could be a potent bone-remodeling signal but the physiological meaning of this property remains to be more ascertained. J. Cell. Biochem. 117: 2559-2569, 2016. © 2016 Wiley Periodicals, Inc.

Isolation of novel PSII-LHCII megacomplexes from pea plants characterized by a combination of proteomics and electron microscopy.

In higher plants, photosystem II (PSII) is a multi-subunit pigment-protein complex embedded in the thylakoid membranes of chloroplasts, where it is present mostly in dimeric form within the grana. Its light-harvesting antenna system, LHCII, is composed of trimeric and monomeric complexes, which can associate in variable number with the dimeric PSII core complex in order to form different types of PSII-LHCII supercomplexes. Moreover, PSII-LHCII supercomplexes can laterally associate within the thylakoid membrane plane, thus forming higher molecular mass complexes, termed PSII-LHCII megacomplexes (Boekema et al. 1999a, in Biochemistry 38:2233-2239; Boekema et al. 1999b, in Eur J Biochem 266:444-452). In this study, pure PSII-LHCII megacomplexes were directly isolated from stacked pea thylakoid membranes by a rapid single-step solubilization, using the detergent n-dodecyl-α-D-maltoside, followed by sucrose gradient ultracentrifugation. The megacomplexes were subjected to biochemical and structural analyses. Transmission electron microscopy on negatively stained samples, followed by single-particle analyses, revealed a novel form of PSII-LHCII megacomplexes, as compared to previous studies (Boekema et al.1999a, in Biochemistry 38:2233-2239; Boekema et al. 1999b, in Eur J Biochem 266:444-452), consisting of two PSII-LHCII supercomplexes sitting side-by-side in the membrane plane, sandwiched together with a second copy. This second copy of the megacomplex is most likely derived from the opposite membrane of a granal stack. Two predominant forms of intact sandwiched megacomplexes were observed and termed, according to (Dekker and Boekema 2005 Biochim Biophys Acta 1706:12-39), as (C2S2)4 and (C2S2 + C2S2M2)2 megacomplexes. By applying a gel-based proteomic approach, the protein composition of the isolated megacomplexes was fully characterized. In summary, the new structural forms of isolated megacomplexes and the related modeling performed provide novel insights into how PSII-LHCII supercomplexes may bind to each other, not only in the membrane plane, but also between granal stacks within the chloroplast.

Characterization of the Volatile and Nonvolatile Fractions of Heartwood Aqueous Extract from Pterocarpus marsupium and Evaluation of Its Cytotoxicity against Cancer Cell Lines.

Pterocarpus marsupium is a well-known plant due to its healing properties, in particular, the use of its aqueous extract is able to reduce blood sugar levels and blood triglyceride concentrations. Although this plant has already been widely studied, a complete characterization of its aqueous extract has not been reported. The present study deals with the characterization of the aqueous extract of P. marsupium in order to obtain a full fingerprint of the volatile and nonvolatile constituents. The volatile constituents were identified by CG-MS, whereas the nonvolatile fraction was characterized by UHPLC-MS/MS using a nontarget approach. Several compounds were identified, in particular, polyphenolic species belonging to the class of proanthocyanidins. Cytotoxicity tests were carried out on four different cancer cell lines and three different non-tumoral cell lines. Preliminary results indicate a selective cytotoxicity of the aqueous extract towards the cancer cells. The potential cytotoxicity due to the presence of metals in the aqueous extract was ruled out by testing an aqueous mixture of the metals at the same concentration found in the P. marsupium extract.

Identification of sulforhodamine B photodegradation products present in nonpermanent tattoos by micro liquid chromatography coupled with tandem high-resolution mass spectrometry.

This article deals with the photodegradation of sulforhodamine B, a dye widely used in nonpermanent tattoos. Degradation evidence was obtained from both aqueous and sweat-simulating solutions of the dye after 9 days of Solarbox irradiation. The identification of the degradation products was achieved using a nontarget approach. For this purpose, a micro liquid chromatography method coupled with tandem high-resolution mass spectrometry was developed. In addition, the chemical structures of five degradation products and two dye impurities were elucidated. The degradation products were the same for both types of solution, whereas the degradation rate of the dye in sweat-simulating solution was slightly faster than that in aqueous solution. The method was also applied to samples of tattooed pigskin subjected to irradiation, in order to better simulate the irradiation effects on the dye used on the skin. None of the degradation products found in the sulforhodamine B solutions were identified in the degraded tattooed pigskin samples, but a new signal at m/z 637.3051 (positive ionization) was found, and the structure of the corresponding molecule was elucidated. The mutagenicity of the photodegradation products was evaluated using a quantitative structure-activity relationship approach, which gave negative results for all the structures elucidated. Graphical Abstract Comparison between tattoed pigskin before and after photodegration process. Strategies for the identification of sulforhodamine B degradation products.

Determination of eight polyphenols and pantothenic acid in extra-virgin olive oil samples by a simple, fast, high-throughput and sensitive ultra high performance liquid chromatography with tandem mass spectrometry method.

A new ultra high performance liquid chromatography coupled with tandem mass spectrometry method for a fast and sensitive determination of eight polyphenols (hydroxytyrosol, catechin, epicatechin, epigallocatechin gallate, oleuropein, quercetin, rutin, tyrosol) and panthotenic acid in extra-virgin olive oil was developed. The method does not require long sample pre-treatment and presents the lowest limit of detection and limit of quantitation values present in literature. Inter- and intra-day variability, linear dynamic range of the calibration curve, recovery and matrix effect were also determined and investigated. The method was applied to several oil samples of different type and origin. Given its accuracy, precision and rapidity, the method is characterized by an interestingly high throughput, reliability, and sensitivity.

Non-targeted identification of tianeptine photodegradation products in water samples by UHPLC-QTOF MS/MS.

This study aims the characterization of several tianeptine transformation products in ultrapure water by simulated sunlight irradiation. Tianeptine was completely degraded after 106 h of exposition following pseudo-first-order kinetics (half-life time = 12.0 ± 2.4 h). Furthermore, an ultra-high-performance liquid chromatography coupled with a high-resolution quadrupole time-of-flight-mass spectrometry method was developed and fully validated taking into account different method performance parameters for the quantification of tianeptine in river water up to a concentration of 400 pg L-1. Following a non-targeted approach based on mass data-independent acquisition, eight different transformation products not previously reported in the literature were identified and accordingly elucidated, proposing a photodegradation mechanism based on the accurate tandem mass spectrometry information acquired. Irradiation experiments were replicated for a tianeptine solution prepared in a blank river water sample, resulting in the formation of the same transformation products and similar degradation kinetics. In addition, a toxicity assessment of the photoproducts was performed by in silico method, being generally all TPs of comparable toxicity to the precursor except for TP1, and showing a similar persistence in the environment except for TP2 and TP6, while TP4 was the only TP predicted as mutagenic. The developed method was applied for the analysis of four river water samples.

Qualitative Metabolite Profiling of Orchis purpurea Huds. by GC and UHPLC/MS Approaches.

Orchids are experiencing wide success in ornamental, medicinal, and food fields. The reason for their success is correlated with both their morphology and metabolomics, the latter linked to their taste and biological effects. Despite many orchids having already been the subject of chemotaxonomic works, some of them are still untapped, like the case of Orchis purpurea. O. purpurea is one of the most common species of the genus Orchis, present in hedgerows, verges, and light woodland, where it is one of the few herbaceous plants able to be unpleasant to herbivorous animals. Essential oil from roots, stems, leaves, and flowers were analyzed via GC/MS analyses, revealing the presence of 70 compounds, with a clear prevalence of coumarin. The high concentration of this metabolite may explain the resistance of O. purpurea to herbivores, being associated with appetite-suppressing properties and a bitter taste. Non-volatile fractions were analyzed via UHPLC-MS analysis revealing the presence of hydroxycinnamic acid derivatives, polyphenols, and glycosidic compounds, probably responsible for their color and fragrance. Taken together, the herein presented results shed light on both the defensive strategy and the chemotaxonomy of O. purpurea.

Simultaneous determination of sixteen underivatized biogenic amines in human urine by HPLC-MS/MS.

The broad group of biogenic amines includes polyamines and catecholamines, whose presence in human tissues and biological fluids can give important diagnostic information and act as marker of many pathologies. In particular, polyamines are involved in cancer cell growth while catecholamines act as neurotransmitters and hormones. Their simultaneous determination in biological tissues and fluids is therefore an important task. A high-performance liquid chromatography tandem mass spectrometry method is presented here for the simultaneous determination in urine of 16 biogenic amines: adrenaline (epinephrine), agmatine, cadaverine, dopamine, histamine, 3-methoxytyramine, noradrenaline (norepinephrine), norephedrine, octopamine, 2-phenylethylamine, putrescine, serotonin, spermidine, spermine, tryptamine, and tyramine. The method does not require any derivatization step. To guarantee the maximum of sensitivity, the mass spectrometer works in selected reaction monitoring mode, monitoring for each analyte the two most intensive transitions. Method validation includes the evaluation of limits of detection (that range from 0.3 to 6.6 µg L(-1)), limits of quantitation (that range from 1.0 to 21.9 µg L(-1)), linearity range (three orders of magnitude), recovery, intra- and inter-day precision on both concentration, and retention time. Recovery (R) is shown not to depend on the analyte concentration: the average R percent ranges from 72.9 to 100.0 %. Particular attention is devoted to the matrix effect and the correlated phenomena of ion enhancement or suppression in mass spectrometry detection.

Correction: Alfei et al. 4-Hydroxybenzoic Acid as an Antiviral Product from Alkaline Autoxidation of Catechinic Acid: A Fact to Be Reviewed. Plants 2022, 11, 1822.

In the original publication [...].

4-Hydroxybenzoic Acid as an Antiviral Product from Alkaline Autoxidation of Catechinic Acid: A Fact to Be Reviewed.

The dark brown mixture resulting from the autooxidation of catechinic acid (CA) (AOCA) has been reported to possess antiviral activity against Herpes Simplex Virus 1 and 2 (HSV-1 and HSV-2). Unfortunately, the constituents of AOCA were not separated or identified and the compound(s) responsible for AOCA's antiviral activity remained unknown until recently. Colorless 4-hydroxy benzoic acid (4-HBA) has been reported as the main constituent (75%) of AOCA, and as being responsible for its antiviral activity. The findings seemed not to be reliable because of the existence in the literature of very different findings, because of the high concentration that was attributed to the supposed 4-HBA in the dark mixture, and because of the absence of essential analytical experiments to confirm 4-HBA in AOCA. Particularly, the AOCA chromatograms highlighting a peak attributable to 4-HBA, using commercial 4-HBA as a standard, is missing, as well as investigations concerning the antiviral activity of marketed 4-HBA. Therefore, in this study, to verify the exactness of the recent reports, we prepared CA from catechin and AOCA from CA, and the absence of 4-HBA in the mixture was first established by thin-layer chromatography (TLC), and then was confirmed by UHPLC­MS/MS, UV­Vis, and ATR­FTIR analyses. For further confirmation, the ATR­FTIR spectral data were processed by principal components analysis (PCA), which unequivocally established strong structural differences between 4-HBA and AOCA. Finally, while the antiviral effects of AOCA against HSV-2 were confirmed, a commercial sample of 4-HBA was completely inactive.