Grapevine and Wine Metabolomics-Based Guidelines for FAIR Data and Metadata Management.

In the era of big and omics data, good organization, management, and description of experimental data are crucial for achieving high-quality datasets. This, in turn, is essential for the export of robust results, to publish reliable papers, make data more easily available, and unlock the huge potential of data reuse. Lately, more and more journals now require authors to share data and metadata according to the FAIR (Findable, Accessible, Interoperable, Reusable) principles. This work aims to provide a step-by-step guideline for the FAIR data and metadata management specific to grapevine and wine science. In detail, the guidelines include recommendations for the organization of data and metadata regarding (i) meaningful information on experimental design and phenotyping, (ii) sample collection, (iii) sample preparation, (iv) chemotype analysis, (v) data analysis (vi) metabolite annotation, and (vii) basic ontologies. We hope that these guidelines will be helpful for the grapevine and wine metabolomics community and that it will benefit from the true potential of data usage in creating new knowledge being revealed.

Quinones as Strecker degradation reagents in wine oxidation processes.

The Strecker aldehydes formed during the reaction between α-amino acids (phenylalanine or methionine) and either gallic acid, caffeic acid or (+)-catechin ortho-quinones were evaluated in wine-model systems. It was demonstrated that phenylacetaldehyde was formed by quinone intermediates at wine pH. The highest amounts of phenylacetaldehyde during the 10days of experiment (69±5µg/L/day; 7x>Control) were obtained from (+) catechin, followed by gallic acid (61±4µg/L/day; 6x>Control) and caffeic acid (41±4µg/L/day; 4x>Control). The intermediate structures delivered from the reaction of ortho-quinones with α-amino acids were demonstrated by MSn.

Monitoring alcoholic fermentation: an untargeted approach.

This work describes the utility and efficiency of a metabolic profiling pipeline that relies on an unsupervised and untargeted approach applied to a HS-SPME/GC-MS data. This noninvasive and high throughput methodology enables "real time" monitoring of the metabolic changes inherent to the biochemical dynamics of a perturbed complex biological system and the extraction of molecular candidates that are latter validated on its biochemical context. To evaluate the efficiency of the pipeline five different fermentations, carried on a synthetic media and whose perturbation was the nitrogen source, were performed in 5 and 500 mL. The smaller volume fermentations were monitored online by HS-SPME/GC-MS, allowing to obtain metabolic profiles and molecular candidates time expression. Nontarget analysis was applied using MS data in two ways: (i) one dimension (1D), where the total ion chromatogram per sample was used, (ii) two dimensions (2D), where the integrity time vs m/z per sample was used. Results indicate that the 2D procedure captured the relevant information more efficiently than the 1D. It was also seen that although there were differences in the fermentation performance in different scales, the metabolic pathways responsible for production of metabolites that impact the quality of the volatile fraction was unaffected, so the proposed pipeline is suitable for the study of different fermentation systems that can undergo subsequent sensory validation on a larger scale.

Instrumental and sensory approaches for the characterization of compounds responsible for wine aroma.

More than 800 aromatic compounds have been identified in wine, some of them at the ng/l level. Wine, therefore, constitutes a very complex matrix, from which it is difficult to isolate a specific aroma character. Gas chromatography-olfactometry (GC-O) applied to wine extracts is used to characterize odor-active zones that are often treated in a hierarchical way by Aroma Extract Dilution Analysis (AEDA). The aromatic impact of the volatiles is evaluated, generally by determining perception thresholds. This methodology has provided convincing results concerning wine flavors, but it does have its limitations. For instance, data on beta-damascenone have demonstrated that these methods could reach their limits for this volatile, in particular, because of the non-quantitative representation of aroma extracts of wines, and because of the difficulty to accurately determine the perception threshold in wines for a compound already present. For beta-damascenone, we have shown that its very low detection threshold with GC-O, its wide range, and its dependence on the composition of the medium resulted in overestimating its direct impact on the aroma of wine. Another way to facilitate the characterization of aromatic compounds was, therefore, investigated. High-Performance Liquid Chromatography (HPLC) methods were developed for the analysis of wine extracts. From an aromatic extract, 25 fractions with various flavors were thus obtained, and reverse-phase methodology was used for the selection and characterization of red- and black-fruit aromas in red wines.

Reactivity of paraquat with sodium salicylate: formation of stable complexes.

Sodium salicylate (NaSAL) has been shown to be a promising antidote for the treatment of paraquat (PQ) poisonings. The modulation of the pro-oxidant and pro-inflammatory pathways, as well as the anti-thrombogenic properties of NaSAL are probably essential features for the healing effects provided by this drug. Nevertheless, a possible direct chemical reactivity between PQ and NaSAL is also a putative pathway to be considered, this hypothesis being the ground of the present study. In accordance, it is shown, for the first time that PQ and NaSAL react immediately in aqueous medium and within 2-3 min in the solid state. Photographs and scanning electron photomicrographs indicated that a new chemical entity is formed when both compounds are mixed. This assumption was corroborated by the evaluation of the melting point, and through several analytical techniques, namely ultraviolet/visible spectroscopy, nuclear magnetic resonance spectroscopy, gas chromatography/mass spectrometry/mass spectrometry (GC/MS/MS), liquid chromatography/electrospray ionization/mass spectrometry/mass spectrometry (LC/ESI/MS/MS) and infrared spectroscopy, which revealed that stable charge-transfer complexes are formed when PQ is mixed with NaSAL. LC/ESI/MS/MS allowed obtaining the stoichiometry of the charge-transfer complexes. In order to increase resolution, single value decomposition, acting as a filter, showed that the charge-transfer complexes with m/z 483, 643 and 803 correspond to the pseudo-molecular ions, respectively 1:2, 1:3 and 1:4 (PQ:NaSAL). In conclusion, these results provided a new and important mechanism of action of NaSAL against the toxicity mediated by PQ.

Kinetics of oxidative degradation of white wines and how they are affected by selected technological parameters.

The negative effects of oxygen on white wine quality and the various factors which influence it (including temperature, dissolved oxygen, pH, and free SO(2)) are well documented both at the sensory and compositional levels. What is less defined is the quantitative relationship between these parameters and the kinetics of the development of the negative effects of oxidation. The experiment presented here attempts to generate data which can be used to predictively model the oxidative degradation of white wines. Bottled wines were submitted to extreme conditions (45 degrees C temperature, O(2) saturation) during 3 months witth samples taken every 15 days for both sensorial and chemical analysis (GC-O/FPD/MS, 420 nm). The synergistic effects of increasing temperature and O(2) at lower pH are evident, both on the decrease in levels of terpene alcohols and norisoprenoids (which impart floral aromas), and on the development of off-flavors such as "honey-like", "boiled-potato", and "farm-feed" associated with the presence of phenylacetaldehyde, methional, and 1,1,6-trimethyl-1,2-dihydronaphthalene.