Advanced mass spectrometry-based foodomics and imaging.

The food analysis has rapidly transcended traditional boundaries and become a multidisciplinary food and nutrition science. Technological advances, particularly in analytical instrumentation, bioinformatics, and sample preparation, enabled development of objective, fast, multiplexed, and deep molecular screenings also for complex samples, such as raw materials and food products. The comprehensive and precise molecular profiles and fingerprints as well as unique molecular markers are determined, both qualitatively and quantitatively, for a broad range of food products with specific sensory properties. Novel analytical platforms and instruments are implemented, methods optimized, and protocols developed for a large number of applications, for instance in food microbiology, toxicology, authentication, food quality control. Modern food analysis technologies enable novel insight and provide good foundations for precise determination of geographical origin, genetically modified food, and differentiation between organic and conventional food. The study of effects of food and nutrition on human health and well-being was facilitated. All enumerated may assist in providing enough safe and quality food to the growing human population, and is possible due to application of foodomics technologies, particularly, genomics, transcriptomics, metabolomics, and proteomics, in food analysis. This review is a comprehensive summary on developments in the fields of food analysis and foodomics from 2014 to 2020 with the emphasis on mass spectrometry (MS)-based analytical platforms and their usage in analysis of food contaminants, proteins, and small molecules. Other foodomics techniques are mentioned in brief. A separate paragraph is dedicated to MS-based imaging technologies in food analysis and foodomics imaging methods, a new emerging technology.

Metabolic Perturbation and Synthetic Biology Strategies for Plant Terpenoid Production—An Updated Overview

Terpenoids represent one of the high-value groups of specialized metabolites with vast structural diversity. They exhibit versatile human benefits and have been successfully exploited in several sectors of day-to-day life applications, including cosmetics, foods, and pharmaceuticals. Historically, the potential use of terpenoids is challenging, and highly hampered by their bioavailability in their natural sources. Significant progress has been made in recent years to overcome such challenges by advancing the heterologous production platforms of hosts and metabolic engineering technologies. Herein, we summarize the latest developments associated with analytical platforms, metabolic engineering, and synthetic biology, with a focus on two terpenoid classes: monoterpenoids and sesquiterpenoids. Accumulated data showed that subcellular localization of both the precursor pool and the introduced enzymes were the crucial factors for increasing the production of targeted terpenoids in plants. We believe this timely review provides a glimpse of current state-of-the-art techniques/methodologies related to terpenoid engineering that would facilitate further improvements in terpenoids research.

Enhancing Cysteine Chemoproteomic Coverage Through Systematic Assessment of Click Chemistry Product Fragmentation

Mass spectrometry-based chemoproteomics has enabled functional analysis and small molecule screening at thousands of cysteine residues in parallel. Widely adopted chemoproteomic sample preparation workflows rely on the use of pan-cysteine reactive probes such as iodoacetamide alkyne combined with biotinylation via copper-catalyzed azide–alkyne cycloaddition (CuAAC) or ‘click chemistry’ for cysteine capture. Despite considerable advances in both sample preparation and analytical platforms, current techniques only sample a small fraction of all cysteines encoded in the human proteome. Extending the recently introduced labile mode of the MSFragger search engine, here we report an in-depth analysis of cysteine biotinylation via click chemistry (CBCC) reagent gas-phase fragmentation during MS/MS analysis. We find that CBCC conjugates produce both known and novel diagnostic fragments and peptide remainder ions. Among these species, we identified a candidate signature ion for CBCC peptides, the oxonium-biotin fragment ion that is generated upon fragmentation of the N(triazole)–C(alkyl) bond together with cyclization. Guided by our empirical comparison of the fragmentation patterns of five CBCC reagent combinations, we achieved enhanced coverage of cysteine labeled peptides. For larger, fragmentation-prone biotinylation reagents, implementation of labile search afforded unique PSMs and provides a roadmap for the utility of such searches in enhancing chemoproteomic peptide coverage.

Toxicometabolomics: Small Molecules to Answer Big Toxicological Questions

Given the high biological impact of classical and emerging toxicants, a sensitive and comprehensive assessment of the hazards and risks of these substances to organisms is urgently needed. In this sense, toxicometabolomics emerged as a new and growing field in life sciences, which use metabolomics to provide new sets of susceptibility, exposure, and/or effects biomarkers; and to characterize in detail the metabolic responses and altered biological pathways that various stressful stimuli cause in many organisms. The present review focuses on the analytical platforms and the typical workflow employed in toxicometabolomic studies, and gives an overview of recent exploratory research that applied metabolomics in various areas of toxicology.

Pharmacometabolomics by NMR in Oncology: A Systematic Review

Pharmacometabolomics (PMx) studies aim to predict individual differences in treatment response and in the development of adverse effects associated with specific drug treatments. Overall, these studies inform us about how individuals will respond to a drug treatment based on their metabolic profiles obtained before, during, or after the therapeutic intervention. In the era of precision medicine, metabolic profiles hold great potential to guide patient selection and stratification in clinical trials, with a focus on improving drug efficacy and safety. Metabolomics is closely related to the phenotype as alterations in metabolism reflect changes in the preceding cascade of genomics, transcriptomics, and proteomics changes, thus providing a significant advance over other omics approaches. Nuclear Magnetic Resonance (NMR) is one of the most widely used analytical platforms in metabolomics studies. In fact, since the introduction of PMx studies in 2006, the number of NMR-based PMx studies has been continuously growing and has provided novel insights into the specific metabolic changes associated with different mechanisms of action and/or toxic effects. This review presents an up-to-date summary of NMR-based PMx studies performed over the last 10 years. Our main objective is to discuss the experimental approaches used for the characterization of the metabolic changes associated with specific therapeutic interventions, the most relevant results obtained so far, and some of the remaining challenges in this area.

Metabolomic Profiling in Lung Cancer: A Systematic Review

Lung cancer continues to be a significant burden worldwide and remains the leading cause of cancer-associated mortality. Two considerable challenges posed by this disease are the diagnosis of 61% of patients in advanced stages and the reduced five-year survival rate of around 4%. Noninvasively collected samples are gaining significant interest as new areas of knowledge are being sought and opened up. Metabolomics is one of these growing areas. In recent years, the use of metabolomics as a resource for the study of lung cancer has been growing. We conducted a systematic review of the literature from the past 10 years in order to identify some metabolites associated with lung cancer. More than 150 metabolites have been associated with lung cancer-altered metabolism. These were detected in different biological samples by different metabolomic analytical platforms. Some of the published results have been consistent, showing the presence/alteration of specific metabolites. However, there is a clear variability due to lack of a full clinical characterization of patients or standardized patients selection. In addition, few published studies have focused on the added value of the metabolomic profile as a means of predicting treatment response for lung cancer. This review reinforces the need for consistent and systematized studies, which will help make it possible to identify metabolic biomarkers and metabolic pathways responsible for the mechanisms that promote tumor progression, relapse and eventually resistance to therapy.

Experimental Characteristics Study of Data Storage Formats for Data Marts Development within Data Lakes

One of the most popular methods for building analytical platforms involves the use of the concept of data lakes. A data lake is a storage system in which the data are presented in their original format, making it difficult to conduct analytics or present aggregated data. To solve this issue, data marts are used, representing environments of stored data of highly specialized information, focused on the requests of employees of a certain department, the vector of an organization’s work. This article presents a study of big data storage formats in the Apache Hadoop platform when used to build data marts.