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Mass Spectrometry Reviews May 2022Determining metabolomic differences among samples of different phenotypes is a critical component of metabolomics research. With the rapid advances in analytical tools... (Review)
Review
Determining metabolomic differences among samples of different phenotypes is a critical component of metabolomics research. With the rapid advances in analytical tools such as ultrahigh-resolution chromatography and mass spectrometry, an increasing number of metabolites can now be profiled with high quantification accuracy. The increased detectability and accuracy raise the level of stringiness required to reduce or control any experimental artifacts that can interfere with the measurement of phenotype-related metabolome changes. One of the artifacts is the batch effect that can be caused by multiple sources. In this review, we discuss the origins of batch effects, approaches to detect interbatch variations, and methods to correct unwanted data variability due to batch effects. We recognize that minimizing batch effects is currently an active research area, yet a very challenging task from both experimental and data processing perspectives. Thus, we try to be critical in describing the performance of a reported method with the hope of stimulating further studies for improving existing methods or developing new methods.
Topics: Mass Spectrometry; Metabolome; Metabolomics
PubMed: 33238061
DOI: 10.1002/mas.21672 -
Methods in Molecular Biology (Clifton,... 2022Obtaining meaningful snapshots of the metabolome of microorganisms requires rapid sampling and immediate quenching of all metabolic activity, to prevent any changes in... (Review)
Review
Obtaining meaningful snapshots of the metabolome of microorganisms requires rapid sampling and immediate quenching of all metabolic activity, to prevent any changes in metabolite levels after sampling. Furthermore, a suitable extraction method is required ensuring complete extraction of metabolites from the cells and inactivation of enzymatic activity, with minimal degradation of labile compounds. Finally, a sensitive, high-throughput analysis platform is needed to quantify a large number of metabolites in a small amount of sample. An issue which has often been overlooked in microbial metabolomics is the fact that many intracellular metabolites are also present in significant amounts outside the cells and may interfere with the quantification of the endo metabolome. Attempts to remove the extracellular metabolites with dedicated quenching methods often induce release of intracellular metabolites into the quenching solution. For eukaryotic microorganisms, this release can be minimized by adaptation of the quenching method. For prokaryotic cells, this has not yet been accomplished, so the application of a differential method whereby metabolites are measured in the culture supernatant as well as in total broth samples, to calculate the intracellular levels by subtraction, seems to be the most suitable approach. Here we present an overview of different sampling, quenching, and extraction methods developed for microbial metabolomics, described in the literature. Detailed protocols are provided for rapid sampling, quenching, and extraction, for measurement of metabolites in total broth samples, washed cell samples, and supernatant, to be applied for quantitative metabolomics of both eukaryotic and prokaryotic microorganisms.
Topics: Metabolome; Metabolomics; Research Design
PubMed: 34718989
DOI: 10.1007/978-1-0716-1585-0_2 -
Current Molecular Medicine 2022Metabolomics is an omics approach of systems biology that involves the development and assessment of large-scale, comprehensive biochemical analysis tools for... (Review)
Review
Metabolomics is an omics approach of systems biology that involves the development and assessment of large-scale, comprehensive biochemical analysis tools for metabolites in biological systems. This review describes the metabolomics workflow and provides an overview of current analytic tools used for the quantification of metabolic profiles. We explain analytic tools such as mass spectrometry (MS), nuclear magnetic resonance (NMR) spectroscopy, ionization techniques, and approaches for data extraction and analysis.
Topics: Mass Spectrometry; Metabolome; Metabolomics; Systems Biology; Workflow
PubMed: 34923941
DOI: 10.2174/1566524022666211217102105 -
SWATH-MS for metabolomics and lipidomics: critical aspects of qualitative and quantitative analysis.Metabolomics : Official Journal of the... Jun 2020While liquid chromatography coupled to mass spectrometric detection in the selected reaction monitoring detection mode offers the best quantification sensitivity for... (Review)
Review
INTRODUCTION
While liquid chromatography coupled to mass spectrometric detection in the selected reaction monitoring detection mode offers the best quantification sensitivity for omics, the number of target analytes is limited, must be predefined and specific methods developed. Data independent acquisition (DIA), including SWATH using quadrupole time of flight or orbitrap mass spectrometers and generic acquisition methods, has emerged as a powerful alternative technique for quantitative and qualitative analyses since it can cover a wide range of analytes without predefinition.
OBJECTIVES
Here we review the current state of DIA, SWATH-MS and highlight novel acquisition strategies for metabolomics and lipidomics and opportunities for data analysis tools.
METHOD
Different databases were searched for papers that report developments and applications of DIA and in particular SWATH-MS in metabolomics and lipidomics.
RESULTS
DIA methods generate digital sample records that can be mined retrospectively as further knowledge is gained and, with standardized acquisition schemes, used in multiple studies. The different chemical spaces of metabolites and lipids require different specificities, hence different acquisition and data processing approaches must be considered for their analysis.
CONCLUSIONS
Although the hardware and acquisition modes are well defined for SWATH-MS, a major challenge for routine use remains the lack of appropriate software tools capable of handling large datasets and large numbers of analytes.
Topics: Animals; Chromatography, High Pressure Liquid; Chromatography, Liquid; Databases, Factual; Humans; Lipidomics; Lipids; Metabolome; Metabolomics; Retrospective Studies; Software; Tandem Mass Spectrometry
PubMed: 32504120
DOI: 10.1007/s11306-020-01692-0 -
Molecules (Basel, Switzerland) Jun 2022The authors of this paper conducted a comparative metabolomic analysis of (OS), providing the metabolic profiles of the stroma (OSBSz) and sclerotia (OSBSh) of OS by...
The authors of this paper conducted a comparative metabolomic analysis of (OS), providing the metabolic profiles of the stroma (OSBSz) and sclerotia (OSBSh) of OS by widely targeted metabolomics and untargeted metabolomics. The results showed that 778 and 1449 metabolites were identified by the widely targeted metabolomics and untargeted metabolomics approaches, respectively. The metabolites in OSBSz and OSBSh are significantly differentiated; 71 and 96 differentially expressed metabolites were identified by the widely targeted metabolomics and untargeted metabolomics approaches, respectively. This suggests that these 71 metabolites (riboflavine, tripdiolide, bromocriptine, lumichrome, tetrahymanol, citrostadienol, etc.) and 96 metabolites (sancycline, vignatic acid B, pirbuterol, rubrophen, epalrestat, etc.) are potential biomarkers. 4-Hydroxybenzaldehyde, arginine, and lumichrome were common differentially expressed metabolites. Using the widely targeted metabolomics approach, the key pathways identified that are involved in creating the differentiation between OSBSz and OSBSh may be nicotinate and nicotinamide metabolism, thiamine metabolism, riboflavin metabolism, glycine, serine, and threonine metabolism, and arginine biosynthesis. The differentially expressed metabolites identified using the untargeted metabolomics approach were mainly involved in arginine biosynthesis, terpenoid backbone biosynthesis, porphyrin and chlorophyll metabolism, and cysteine and methionine metabolism. The purpose of this research was to provide support for the assessment of the differences between the stroma and sclerotia, to furnish a material basis for the evaluation of the physical effects of OS, and to provide a reference for the selection of detection methods for the metabolomics of OS.
Topics: Arginine; Biomarkers; Cordyceps; Metabolome; Metabolomics
PubMed: 35684580
DOI: 10.3390/molecules27113645 -
Expert Review of Proteomics Jan 2021ABSTACT Metabolomics, one of the most high-promising technologies, is the most recently developed post-genomics discipline for developing new diagnostic tests for future... (Review)
Review
ABSTACT Metabolomics, one of the most high-promising technologies, is the most recently developed post-genomics discipline for developing new diagnostic tests for future implementation in medicine. More than 2,000 scientific papers, using mass spectrometry-based (MS-based) metabolomics analysis for human disease diagnostics, have been published during the past two decades, and almost every metabolomics study shows high diagnostic accuracy. However, despite the great results and promising perspectives, there are currently no diagnostic tests based on metabolomics that have been approved and introduced into clinics. In this report, the advantages and challenges of MS-based metabolomics are discussed with a focus on its developing role in diagnostics, and the current trends in implementing metabolomics diagnostics in the clinic. In the development of new clinical diagnostics tests, MS-based metabolomics has potential as both a preliminary discovery base for routine testing and a multi-test prototype, which is hoped to be introduced into clinical practice in the near future. A laboratory-developed test (LDT) is one possible way that multi-testing could be developed.
Topics: Humans; Mass Spectrometry; Metabolome; Metabolomics; Pathology, Molecular
PubMed: 33653222
DOI: 10.1080/14789450.2021.1893695 -
Cell Host & Microbe Apr 2023Increasing experimental evidence suggests that administering live commensal bacterial species can optimize microbiome composition and lead to reduced disease severity... (Review)
Review
Increasing experimental evidence suggests that administering live commensal bacterial species can optimize microbiome composition and lead to reduced disease severity and enhanced health. Our understanding of the intestinal microbiome and its functions has increased over the past two decades largely due to deep sequence analyses of fecal nucleic acids, metabolomic and proteomic assays to measure nutrient use and metabolite production, and extensive studies on the metabolism and ecological interactions of a wide range of commensal bacterial species inhabiting the intestine. Herein, we review new and important findings that have emerged from this work and provide thoughts and considerations on approaches to re-establish and optimize microbiome functions by assembling and administering commensal bacterial consortia.
Topics: Metabolome; Proteomics; Microbiota; Feces; Metabolomics; Bacteria
PubMed: 37054670
DOI: 10.1016/j.chom.2023.03.002 -
Cellular and Molecular Life Sciences :... Oct 2021During the past decade metabolomics has emerged as one of the fastest developing branches of "-omics" technologies. Metabolomics involves documentation, identification,... (Review)
Review
During the past decade metabolomics has emerged as one of the fastest developing branches of "-omics" technologies. Metabolomics involves documentation, identification, and quantification of metabolites through modern analytical platforms in various biological systems. Advanced analytical tools, such as gas chromatography-mass spectrometry (GC/MS), liquid chromatography-mass spectroscopy (LC/MS), and non-destructive nuclear magnetic resonance (NMR) spectroscopy, have facilitated metabolite profiling of complex biological matrices. Metabolomics, along with transcriptomics, has an influential role in discovering connections between genetic regulation, metabolite phenotyping and biomarkers identification. Comprehensive metabolite profiling allows integration of the summarized data towards manipulation of biosynthetic pathways, determination of nutritional quality markers, improvement in crop yield, selection of desired metabolites/genes, and their heritability in modern breeding. Along with that, metabolomics is invaluable in predicting the biological activity of medicinal plants, assisting the bioactivity-guided fractionation process and bioactive leads discovery, as well as serving as a tool for quality control and authentication of commercial plant-derived natural products. Metabolomic analysis of human biofluids is implemented in clinical practice to discriminate between physiological and pathological state in humans, to aid early disease biomarker discovery and predict individual response to drug therapy. Thus, metabolomics could be utilized to preserve human health by improving the nutritional quality of crops and accelerating plant-derived bioactive leads discovery through disease diagnostics, or through increasing the therapeutic efficacy of drugs via more personalized approach. Here, we attempt to explore the potential value of metabolite profiling comprising the above-mentioned applications of metabolomics in crop improvement, medicinal plants utilization, and, in the prognosis, diagnosis and management of complex diseases.
Topics: Animals; Biological Products; Biomarkers; Crops, Agricultural; Humans; Metabolome; Metabolomics; Pharmaceutical Preparations
PubMed: 34410445
DOI: 10.1007/s00018-021-03918-3 -
Trends in Microbiology Jul 2022Among the diverse metabolites produced by microbial communities, some are volatile. Volatile organic compounds (VOCs) are vigorously cycled by microbes as metabolic... (Review)
Review
Among the diverse metabolites produced by microbial communities, some are volatile. Volatile organic compounds (VOCs) are vigorously cycled by microbes as metabolic substrates and products and as signaling molecules. Yet, current microbial metabolomic studies predominantly focus on nonvolatile metabolites and overlook VOCs, which therefore represent a missing component of the metabolome. Advances in VOC detection now allow simultaneous observation of the numerous VOCs constituting the 'volatilome' of microbial systems. We present a roadmap for integrating and advancing VOC and other 'omics approaches and highlight the potential for realtime VOC measurements to help overcome limitations in discrete 'omics sampling. Including volatile metabolites in metabolomics, both conceptually and in practice, will build a more comprehensive understanding of microbial processes across ecological communities.
Topics: Metabolome; Metabolomics; Microbiota; Volatile Organic Compounds
PubMed: 35039213
DOI: 10.1016/j.tim.2021.12.004 -
Advances in Experimental Medicine and... 2023Highly selective and sensitive analytical techniques are necessary for microbial metabolomics due to the complexity of the microbial sample matrix. Hence, mass...
Highly selective and sensitive analytical techniques are necessary for microbial metabolomics due to the complexity of the microbial sample matrix. Hence, mass spectrometry (MS) has been successfully applied in microbial metabolomics due to its high precision, versatility, sensitivity, and wide dynamic range. The different analytical tools using MS have been employed in microbial metabolomics investigations and can contribute to the discovery or accelerate the search for bioactive substances. The coupling with chromatographic and electrophoretic separation techniques has resulted in more efficient technologies for the analysis of microbial compounds occurring in trace levels. This book chapter describes the current advances in the application of mass spectrometry-based metabolomics in the search for new biologically active agents from microbial sources; the development of new approaches for in silico annotation of natural products; the different technologies employing mass spectrometry imaging to deliver more comprehensive analysis and elucidate the metabolome involved in ecological interactions as they enable visualization of the spatial dispersion of small molecules. We also describe other ambient ionization techniques applied to the fingerprint of microbial natural products and modern techniques such as ion mobility mass spectrometry used to microbial metabolomic analyses and the dereplication of natural microbial products through MS.
Topics: Mass Spectrometry; Metabolomics; Metabolome; Biological Products
PubMed: 37843807
DOI: 10.1007/978-3-031-41741-2_5