SECIMTools: a suite of metabolomics data analysis tools

Rapid QC-MS: Interactive Dashboard for Synchronous Mass Spectrometry Data Acquisition Quality Control

Consistently collecting high-quality liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) data is a time-consuming hurdle for untargeted workflows. Analytical controls such as internal and biological standards are commonly included in high-throughput workflows, helping researchers recognize low-integrity specimens regardless of their biological source. However, evaluating these standards as data are collected has remained a considerable bottleneck─in both person-hours and accuracy. Here we present Rapid QC-MS, an automated, interactive dashboard for assessing LC-MS/MS data quality. Minutes after a new data file is written, a browser-viewable dashboard is updated with quality control results spanning multiple performance dimensions such as instrument sensitivity, in-run retention time shifts, and mass accuracy drift. Rapid QC-MS provides interactive visualizations that help users recognize acute deviations in these performance metrics, as well as gradual drifts over periods of hours, days, months, or years. Rapid QC-MS is open-source, simple to install, and highly configurable. By integrating open-source Python libraries and widely used MS analysis software, it can adapt to any LC-MS/MS workflow. Rapid QC-MS runs locally and offers optional remote quality control by syncing with Google Drive. Furthermore, Rapid QC-MS can operate in a semiautonomous fashion, alerting users to specimens with potentially poor analytical integrity via frequently used messaging applications. Initially developed for integration with Thermo Orbitrap workflows, Rapid QC-MS offers a fast, straightforward approach to help users collect high-quality untargeted LC-MS/MS data by eliminating many of the most time-consuming steps in manual data curation. Download for free: https://github.com/czbiohub-sf/Rapid-QC-MS.

Untargeted Metabolomic Analysis of Lactation-Stage-Matched Human and Bovine Milk Samples at 2 Weeks Postnatal

Epidemiological data demonstrate that bovine whole milk is often substituted for human milk during the first 12 months of life and may be associated with adverse infant outcomes. The objective of this study is to interrogate the human and bovine milk metabolome at 2 weeks of life to identify unique metabolites that may impact infant health outcomes. Human milk (n = 10) was collected at 2 weeks postpartum from normal-weight mothers (pre-pregnant BMI < 25 kg/m2) that vaginally delivered term infants and were exclusively breastfeeding their infant for at least 2 months. Similarly, bovine milk (n = 10) was collected 2 weeks postpartum from normal-weight primiparous Holstein dairy cows. Untargeted data were acquired on all milk samples using high-resolution liquid chromatography-high-resolution tandem mass spectrometry (HR LC-MS/MS). MS data pre-processing from feature calling to metabolite annotation was performed using MS-DIAL and MS-FLO. Our results revealed that more than 80% of the milk metabolome is shared between human and bovine milk samples during early lactation. Unbiased analysis of identified metabolites revealed that nearly 80% of milk metabolites may contribute to microbial metabolism and microbe-host interactions. Collectively, these results highlight untargeted metabolomics as a potential strategy to identify unique and shared metabolites in bovine and human milk that may relate to and impact infant health outcomes.

Statistical methods and resources for biomarker discovery using metabolomics

Metabolomics is a dynamic tool for elucidating biochemical changes in human health and disease. Metabolic profiles provide a close insight into physiological states and are highly volatile to genetic and environmental perturbations. Variation in metabolic profiles can inform mechanisms of pathology, providing potential biomarkers for diagnosis and assessment of the risk of contracting a disease. With the advancement of high-throughput technologies, large-scale metabolomics data sources have become abundant. As such, careful statistical analysis of intricate metabolomics data is essential for deriving relevant and robust results that can be deployed in real-life clinical settings. Multiple tools have been developed for both data analysis and interpretations. In this review, we survey statistical approaches and corresponding statistical tools that are available for discovery of biomarkers using metabolomics.

A Metabolomics and Big Data Approach to Cannabis Authenticity (Authentomics)

With the increasing accessibility of cannabis (Cannabis sativa L., also known as marijuana and hemp), its products are being developed as extracts for both recreational and therapeutic use. This has led to increased scrutiny by regulatory bodies, who aim to understand and regulate the complex chemistry of these products to ensure their safety and efficacy. Regulators use targeted analyses to track the concentration of key bioactive metabolites and potentially harmful contaminants, such as metals and other impurities. However, the metabolic complexity of cannabis metabolic pathways requires a more comprehensive approach. A non-targeted metabolomic analysis of cannabis products is necessary to generate data that can be used to determine their authenticity and efficacy. An authentomics approach, which involves combining the non-targeted analysis of new samples with big data comparisons to authenticated historic datasets, provides a robust method for verifying the quality of cannabis products. To meet International Organization for Standardization (ISO) standards, it is necessary to implement the authentomics platform technology and build an integrated database of cannabis analytical results. This study is the first to review the topic of the authentomics of cannabis and its potential to meet ISO standards.

An anchored experimental design and meta-analysis approach to address batch effects in large-scale metabolomics

Untargeted metabolomics studies are unbiased but identifying the same feature across studies is complicated by environmental variation, batch effects, and instrument variability. Ideally, several studies that assay the same set of metabolic features would be used to select recurring features to pursue for identification. Here, we developed an anchored experimental design. This generalizable approach enabled us to integrate three genetic studies consisting of 14 test strains of Caenorhabditis elegans prior to the compound identification process. An anchor strain, PD1074, was included in every sample collection, resulting in a large set of biological replicates of a genetically identical strain that anchored each study. This enables us to estimate treatment effects within each batch and apply straightforward meta-analytic approaches to combine treatment effects across batches without the need for estimation of batch effects and complex normalization strategies. We collected 104 test samples for three genetic studies across six batches to produce five analytical datasets from two complementary technologies commonly used in untargeted metabolomics. Here, we use the model system C. elegans to demonstrate that an augmented design combined with experimental blocks and other metabolomic QC approaches can be used to anchor studies and enable comparisons of stable spectral features across time without the need for compound identification. This approach is generalizable to systems where the same genotype can be assayed in multiple environments and provides biologically relevant features for downstream compound identification efforts. All methods are included in the newest release of the publicly available SECIMTools based on the open-source Galaxy platform.

Postbiotics Prepared Using Lactobacillus paracasei CCFM1224 Prevent Nonalcoholic Fatty Liver Disease by Modulating the Gut Microbiota and Liver Metabolism

Postbiotics are rich in a variety of bioactive components, which may have beneficial effects in inhibiting hepatic lipid accumulation. In this study, we investigated the preventive effects of postbiotics (POST) prepared from Lactobacillus paracasei on non-alcoholic fatty liver disease (NAFLD). Our results showed that when mice ingested a high-fat diet (HFD) and POST simultaneously, weight gain was slowed, epididymal white fat hypertrophy and insulin resistance were suppressed, serum biochemical indicators related to blood lipid metabolism were improved, and hepatic steatosis and liver inflammation decreased. Bacterial sequencing showed that POST modulated the gut microbiota in HFD mice, increasing the relative abundance of Akkermansia and reducing the relative abundance of Lachnospiraceae NK4A136 group, Ruminiclostridium and Bilophila. Spearman’s correlation analysis revealed significant correlations between lipid metabolism parameters and gut microbes. Functional prediction results showed that the regulation of gut microbiota was associated with the improvement of metabolic status. The metabolomic analysis of the liver revealed that POST-regulated liver metabolic pathways, such as glycerophospholipid and ether lipid metabolism, pantothenate and CoA biosynthesis, some parts of amino acid metabolism, and other metabolic pathways. In addition, POST regulated the gene expression in hepatocytes at the mRNA level, thereby regulating lipid metabolism. These findings suggest that POST plays a protective role against NAFLD and may exert its efficacy by modulating the gut microbiota and liver metabolism, and these findings may be applied to related functional foods.

GAIT-GM integrative cross-omics analyses reveal cholinergic defects in a C. elegans model of Parkinson's disease

Parkinson’s disease (PD) is a disabling neurodegenerative disorder in which multiple cell types, including dopaminergic and cholinergic neurons, are affected. The mechanisms of neurodegeneration in PD are not fully understood, limiting the development of therapies directed at disease-relevant molecular targets. C. elegans is a genetically tractable model system that can be used to disentangle disease mechanisms in complex diseases such as PD. Such mechanisms can be studied combining high-throughput molecular profiling technologies such as transcriptomics and metabolomics. However, the integrative analysis of multi-omics data in order to unravel disease mechanisms is a challenging task without advanced bioinformatics training. Galaxy, a widely-used resource for enabling bioinformatics analysis by the broad scientific community, has poor representation of multi-omics integration pipelines. We present the integrative analysis of gene expression and metabolite levels of a C. elegans PD model using GAIT-GM, a new Galaxy tool for multi-omics data analysis. Using GAIT-GM, we discovered an association between branched-chain amino acid metabolism and cholinergic neurons in the C. elegans PD model. An independent follow-up experiment uncovered cholinergic neurodegeneration in the C. elegans model that is consistent with cholinergic cell loss observed in PD. GAIT-GM is an easy to use Galaxy-based tool for generating novel testable hypotheses of disease mechanisms involving gene-metabolite relationships.

Novel Biomarkers of Habitual Alcohol Intake and Associations With Risk of Pancreatic and Liver Cancers and Liver Disease Mortality

BACKGROUND

Alcohol is an established risk factor for several cancers, but modest alcohol-cancer associations may be missed because of measurement error in self-reported assessments. Biomarkers of habitual alcohol intake may provide novel insight into the relationship between alcohol and cancer risk.

METHODS

Untargeted metabolomics was used to identify metabolites correlated with self-reported habitual alcohol intake in a discovery dataset from the European Prospective Investigation into Cancer and Nutrition (EPIC; n = 454). Statistically significant correlations were tested in independent datasets of controls from case-control studies nested within EPIC (n = 280) and the Alpha-Tocopherol, Beta-Carotene Cancer Prevention (ATBC; n = 438) study. Conditional logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for associations of alcohol-associated metabolites and self-reported alcohol intake with risk of pancreatic cancer, hepatocellular carcinoma (HCC), liver cancer, and liver disease mortality in the contributing studies.

RESULTS

Two metabolites displayed a dose-response association with self-reported alcohol intake: 2-hydroxy-3-methylbutyric acid and an unidentified compound. A 1-SD (log2) increase in levels of 2-hydroxy-3-methylbutyric acid was associated with risk of HCC (OR = 2.54, 95% CI = 1.51 to 4.27) and pancreatic cancer (OR = 1.43, 95% CI = 1.03 to 1.99) in EPIC and liver cancer (OR = 2.00, 95% CI = 1.44 to 2.77) and liver disease mortality (OR = 2.16, 95% CI = 1.63 to 2.86) in ATBC. Conversely, a 1-SD (log2) increase in questionnaire-derived alcohol intake was not associated with HCC or pancreatic cancer in EPIC or liver cancer in ATBC but was associated with liver disease mortality (OR = 2.19, 95% CI = 1.60 to 2.98) in ATBC.

CONCLUSIONS

2-hydroxy-3-methylbutyric acid is a candidate biomarker of habitual alcohol intake that may advance the study of alcohol and cancer risk in population-based studies.

A Workflow to Perform Targeted Metabolomics at the Untargeted Scale on a Triple Quadrupole Mass Spectrometer

The thousands of features commonly observed when performing untargeted metabolomics with quadrupole time-of-flight (QTOF) and Orbitrap mass spectrometers often correspond to only a few hundred unique metabolites of biological origin, which is in the range of what can be assayed in a single targeted metabolomics experiment by using a triple quadrupole (QqQ) mass spectrometer. A major benefit of performing targeted metabolomics with QqQ mass spectrometry is the affordability of the instruments relative to high-resolution QTOF and Orbitrap platforms. Optimizing targeted methods to profile hundreds of metabolites on a QqQ mass spectrometer, however, has historically been limited by the availability of authentic standards, particularly for "unknowns" that have yet to be structurally identified. Here, we report a strategy to develop multiple reaction monitoring (MRM) methods for QqQ instruments on the basis of high-resolution spectra, thereby enabling us to use data from untargeted metabolomics to design targeted experiments without the need for authentic standards. We demonstrate that using high-resolution fragmentation data alone to design MRM methods results in the same quantitative performance as when methods are optimized by measuring authentic standards on QqQ instruments, as is conventionally done. The approach was validated by showing that Orbitrap ID-X data can be used to establish MRM methods on a Thermo TSQ Altis and two Agilent QqQs for hundreds of metabolites, including unknowns, without a dependence on standards. Finally, we highlight an application where metabolite profiling was performed on an ID-X and a QqQ by using the strategy introduced here, with both data sets yielding the same result. The described approach therefore allows us to use QqQ instruments, which are often associated with targeted metabolomics, to profile knowns and unknowns at a comprehensive scale that is typical of untargeted metabolomics.

Long-Term Metabolomics Reference Material

The use of quality control samples in metabolomics ensures data quality, reproducibility, and comparability between studies, analytical platforms, and laboratories. Long-term, stable, and sustainable reference materials (RMs) are a critical component of the quality assurance/quality control (QA/QC) system; however, the limited selection of currently available matrix-matched RMs reduces their applicability for widespread use. To produce an RM in any context, for any matrix that is robust to changes over the course of time, we developed iterative batch averaging method (IBAT). To illustrate this method, we generated 11 independently grown Escherichia coli batches and made an RM over the course of 10 IBAT iterations. We measured the variance of these materials by nuclear magnetic resonance (NMR) and showed that IBAT produces a stable and sustainable RM over time. This E. coli RM was then used as a food source to produce a Caenorhabditis elegans RM for a metabolomics experiment. The metabolite extraction of this material, alongside 41 independently grown individual C. elegans samples of the same genotype, allowed us to estimate the proportion of sample variation in preanalytical steps. From the NMR data, we found that 40% of the metabolite variance is due to the metabolite extraction process and analysis and 60% is due to sample-to-sample variance. The availability of RMs in untargeted metabolomics is one of the predominant needs of the metabolomics community that reach beyond quality control practices. IBAT addresses this need by facilitating the production of biologically relevant RMs and increasing their widespread use.

Obesity-Dependent Adipokine Chemerin Suppresses Fatty Acid Oxidation to Confer Ferroptosis Resistance

Clear cell renal cell carcinoma (ccRCC) is characterized by accumulation of neutral lipids and adipogenic transdifferentiation. We assessed adipokine expression in ccRCC and found that tumor tissues and patient plasma exhibit obesity-dependent elevations of the adipokine chemerin. Attenuation of chemerin by several approaches led to significant reduction in lipid deposition and impairment of tumor cell growth in vitro and in vivo. A multi-omics approach revealed that chemerin suppresses fatty acid oxidation, preventing ferroptosis, and maintains fatty acid levels that activate hypoxia-inducible factor 2α expression. The lipid coenzyme Q and mitochondrial complex IV, whose biogeneses are lipid-dependent, were found to be decreased after chemerin inhibition, contributing to lipid reactive oxygen species production. Monoclonal antibody targeting chemerin led to reduced lipid storage and diminished tumor growth, demonstrating translational potential of chemerin inhibition. Collectively, the results suggest that obesity and tumor cells contribute to ccRCC through the expression of chemerin, which is indispensable in ccRCC biology. SIGNIFICANCE: Identification of a hypoxia-inducible factor-dependent adipokine that prevents fatty acid oxidation and causes escape from ferroptosis highlights a critical metabolic dependency unique in the clear cell subtype of kidney cancer. Targeting lipid metabolism via inhibition of a soluble factor is a promising pharmacologic approach to expand therapeutic strategies for patients with ccRCC.See related commentary by Reznik et al., p. 1879.This article is highlighted in the In This Issue feature, p. 1861.

Head, Shoulders, Knees, and Toes: Placement of Wearable Passive Samplers Alters Exposure Profiles Observed

Chemical exposures are a major risk factor for many diseases. Comprehensive characterization of personal exposures is necessary to highlight chemicals of concern and factors that influence these chemical exposure dynamics. For this purpose, wearable passive samplers can be applied to assess longitudinal personal exposures to airborne contaminants. Questions remain regarding the impact of sampler placement at different locations of the body on the exposure profiles observed and how these placements affect the monitoring of seasonal dynamics in exposures. This study assessed personal air contaminant exposure using passive samplers worn in parallel across 32 participant's wrists, chest, and shoes over 24 h. Samplers were analyzed by thermal desorption gas chromatography high-resolution mass spectrometry. Personal exposure profiles were similar for about one-third of the 275 identified chemicals, irrespective of sampler placement. Signals of certain semivolatile organic compounds (SVOCs) were enhanced in shoes and, to a lesser extent, wrist samplers, as compared to those in chest samplers. Signals of volatile organic compounds were less impacted by sampler placement. Results showed that chest samplers predominantly captured more volatile exposures, as compared to those of particle-bound exposures, which may indicate predominant monitoring of chemicals via the inhalation route of exposure for chest samplers. In contrast, shoe samplers were more sensitive to particle-bound SVOCs. Seventy-one chemicals changed across participants between winter and summer in the same manner for two or more different sampler placements on the body, whereas 122 chemicals were observed to have seasonal differences in only one placement. Hence, the placement in certain cases significantly impacts exposure dynamics observed. This work shows that it is essential in epidemiological studies undertaking exposure assessment to consider the consequence of the placement of exposure monitors.

Omics-Driven Biotechnology for Industrial Applications

Biomanufacturing is a key component of biotechnology that uses biological systems to produce bioproducts of commercial relevance, which are of great interest to the energy, material, pharmaceutical, food, and agriculture industries. Biotechnology-based approaches, such as synthetic biology and metabolic engineering are heavily reliant on "omics" driven systems biology to characterize and understand metabolic networks. Knowledge gained from systems biology experiments aid the development of synthetic biology tools and the advancement of metabolic engineering studies toward establishing robust industrial biomanufacturing platforms. In this review, we discuss recent advances in "omics" technologies, compare the pros and cons of the different "omics" technologies, and discuss the necessary requirements for carrying out multi-omics experiments. We highlight the influence of "omics" technologies on the production of biofuels and bioproducts by metabolic engineering. Finally, we discuss the application of "omics" technologies to agricultural and food biotechnology, and review the impact of "omics" on current COVID-19 research.

Exploring the external exposome using wearable passive samplers - The China BAPE study

Environmental exposures are one of the greatest threats to human health, yet we lack tools to answer simple questions about our exposures: what are our personal exposure profiles and how do they change overtime (external exposome), how toxic are these chemicals, and what are the sources of these exposures? To capture variation in personal exposures to airborne chemicals in the gas and particulate phases and identify exposures which pose the greatest health risk, wearable exposure monitors can be deployed. In this study, we deployed passive air sampler wristbands with 84 healthy participants (aged 60-69 years) as part of the Biomarkers for Air Pollutants Exposure (China BAPE) study. Participants wore the wristband samplers for 3 days each month for five consecutive months. Passive samplers were analyzed using a novel gas chromatography high resolution mass spectrometry data-processing workflow to overcome the bottleneck of processing large datasets and improve confidence in the resulting identified features. The toxicity of chemicals observed frequently in personal exposures were predicted to identify exposures of potential concern via inhalation route or other routes of airborne contaminant exposure. Three exposures were highlighted based on elevated toxicity: dichlorvos from insecticides (mosquito/malaria control), naphthalene partly from mothballs, and 183 polyaromatic hydrocarbons from multiple sources. Other exposures explored in this study are linked to diet and personal care products, cigarette smoke, sunscreen, and antimicrobial soaps. We highlight the potential for this workflow employing wearable passive samplers for prioritizing chemicals of concern at both the community and individual level, and characterizing sources of exposures for follow up interventions.

PyIOmica: longitudinal omics analysis and trend identification

SUMMARY

PyIOmica is an open-source Python package focusing on integrating longitudinal multiple omics datasets, characterizing and categorizing temporal trends. The package includes multiple bioinformatics tools including data normalization, annotation, categorization, visualization and enrichment analysis for gene ontology terms and pathways. Additionally, the package includes an implementation of visibility graphs to visualize time series as networks.

AVAILABILITY AND IMPLEMENTATION

PyIOmica is implemented as a Python package (pyiomica), available for download and installation through the Python Package Index (https://pypi.python.org/pypi/pyiomica), and can be deployed using the Python import function following installation. PyIOmica has been tested on Mac OS X, Unix/Linux and Microsoft Windows. The application is distributed under an MIT license. Source code for each release is also available for download on Zenodo (https://doi.org/10.5281/zenodo.3548040).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics.

Metabogenomics reveals four candidate regions involved in the pathophysiology of Equine Metabolic Syndrome

An analogous condition to human metabolic syndrome, Equine Metabolic Syndrome (EMS) is defined by several clinical signs including obesity, hyperinsulinemia, and peripheral insulin dysregulation (ID). Affected horses may also exhibit hypertension, hyperlipemia and systemic inflammation. Measures of ID typically comprise the gold-standard for diagnosis in veterinary care. Yet, the dynamic nature of insulin homeostasis and complex procedures of typical assays make accurate quantification of ID and EMS challenging. This work aimed to investigate new strategies for identification of biochemical markers and correlated genes in EMS. To quantify EMS risk within this population, we utilized a composite score derived from nine common diagnostic variables. We applied a global liquid chromatography/mass spectroscopy approach (HPLC/MS) to whole plasma collected from 49 Arabian horses, resulting in 3392 high-confidence features and identification of putative metabolites in public databases. We performed a genome wide association analysis with genotypes from the 670k Affymetrix Equine SNP array utilizing EMS-correlated metabolites as phenotypes. We discovered four metabolite features significantly correlated with EMS score (P < 1.474 × 10^-5). GWAs for these features results (P = 6.787 × 10^-7, Bonferroni) identified four unique candidate regions (r² > 0.4) containing 63 genes. Significant genomic markers capture 43.52% of the variation in the original EMS score phenotype. The identified genomic loci provide insight into the pathways controlling variation in EMS and the origin of genetic predisposition to the condition. Rapid, feasible and accurate diagnostic tools derived from metabogenomics can be translated into measurable benefits in the timeline and quality of preventative management practices to preserve health in horses.

Perspective: Dietary Biomarkers of Intake and Exposure-Exploration with Omics Approaches

While conventional nutrition research has yielded biomarkers such as doubly labeled water for energy metabolism and 24-h urinary nitrogen for protein intake, a critical need exists for additional, equally robust biomarkers that allow for objective assessment of specific food intake and dietary exposure. Recent advances in high-throughput MS combined with improved metabolomics techniques and bioinformatic tools provide new opportunities for dietary biomarker development. In September 2018, the NIH organized a 2-d workshop to engage nutrition and omics researchers and explore the potential of multiomics approaches in nutritional biomarker research. The current Perspective summarizes key gaps and challenges identified, as well as the recommendations from the workshop that could serve as a guide for scientists interested in dietary biomarkers research. Topics addressed included study designs for biomarker development, analytical and bioinformatic considerations, and integration of dietary biomarkers with other omics techniques. Several clear needs were identified, including larger controlled feeding studies, testing a variety of foods and dietary patterns across diverse populations, improved reporting standards to support study replication, more chemical standards covering a broader range of food constituents and human metabolites, standardized approaches for biomarker validation, comprehensive and accessible food composition databases, a common ontology for dietary biomarker literature, and methodologic work on statistical procedures for intake biomarker discovery. Multidisciplinary research teams with appropriate expertise are critical to moving forward the field of dietary biomarkers and producing robust, reproducible biomarkers that can be used in public health and clinical research.

Re-modeling of foliar membrane lipids in a seagrass allows for growth in phosphorus-deplete conditions

In this study, we used liquid chromatography high-resolution tandem mass spectrometry to analyze the lipidome of turtlegrass (Thalassia testudinum) leaves with either extremely high phosphorus content or extremely low phosphorus content. Most species of phospholipids were significantly down-regulated in phosphorus-deplete leaves, whereas diacylglyceryltrimethylhomoserine (DGTS), triglycerides (TG), galactolipid digalactosyldiacylglycerol (DGDG), certain species of glucuronosyldiacylglycerols (GlcADG), and certain species of sulfoquinovosyl diacylglycerol (SQDG) were significantly upregulated, accounting for the change in phosphorus content, as well as structural differences in the leaves of plants growing across regions of varying elemental availability. These data suggest that seagrasses are able to modify the phosphorus content in leaf membranes dependent upon environmental availability.

A large-scale analysis of targeted metabolomics data from heterogeneous biological samples provides insights into metabolite dynamics

INTRODUCTION

We previously developed a tandem mass spectrometry-based label-free targeted metabolomics analysis framework coupled to two distinct chromatographic methods, reversed-phase liquid chromatography (RPLC) and hydrophilic interaction liquid chromatography (HILIC), with dynamic multiple reaction monitoring (dMRM) for simultaneous detection of over 200 metabolites to study core metabolic pathways.

OBJECTIVES

We aim to analyze a large-scale heterogeneous data compendium generated from our LC-MS/MS platform with both RPLC and HILIC methods to systematically assess measurement quality in biological replicate groups and to investigate metabolite abundance changes and patterns across different biological conditions.

METHODS

Our metabolomics framework was applied in a wide range of experimental systems including cancer cell lines, tumors, extracellular media, primary cells, immune cells, organoids, organs (e.g. pancreata), tissues, and sera from human and mice. We also developed computational and statistical analysis pipelines, which include hierarchical clustering, replicate-group CV analysis, correlation analysis, and case-control paired analysis.

RESULTS

We generated a compendium of 42 heterogeneous deidentified datasets with 635 samples using both RPLC and HILIC methods. There exist metabolite signatures that correspond to various phenotypes of the heterogeneous datasets, involved in several metabolic pathways. The RPLC method shows overall better reproducibility than the HILIC method for most metabolites including polar amino acids. Correlation analysis reveals high confidence metabolites irrespective of experimental systems such as methionine, phenylalanine, and taurine. We also identify homocystine, reduced glutathione, and phosphoenolpyruvic acid as highly dynamic metabolites across all case-control paired samples.

CONCLUSIONS

Our study is expected to serve as a resource and a reference point for a systematic analysis of label-free LC-MS/MS targeted metabolomics data in both RPLC and HILIC methods with dMRM.

"-Omics" workflow for paleolimnological and geological archives: A review

"-Omics" is a powerful screening method with applications in molecular biology, toxicology, wildlife biology, natural product discovery, and many other fields. Genomics, proteomics, metabolomics, and lipidomics are common examples included under the "-omics" umbrella. This screening method uses combinations of untargeted, semi-targeted, and targeted analyses paired with data mining to facilitate researchers' understanding of the genome, proteins, and small organic molecules in biological systems. Recently, however, the use of "-omics" has expanded into the fields of geology, specifically petrology, and paleolimnology. Specifically, untargeted analyses stand to transform these fields as petroleomics, and sediment-"omics" become more prevalent. "-Omics" facilitates the visualization of small molecule profiles from environmental matrices (i.e. oil and sediment). Small molecule profiles can provide improved understanding of small molecules distributions throughout the environment, and how those compositions can change depending on conditions (i.e. climate change, weathering, etc.). "-Omics" also facilities discovery of next-generation biomarkers that can be used for oil source identification and as proxies for reconstructing past environmental changes. Untargeted analyses paired with data mining and multivariate statistical analyses represents a powerful suite of tools for hypothesis generation, and new method development for environmental reconstructions. Here we present an introduction to "-omics" methodology, technical terms, and examples of applications to paleolimnology and petrology. The purpose of this review is to highlight the important considerations at each step in the "-omics" workflow to produce high quality and statistically powerful data for petrological and paleolimnological applications.

Tools and resources for metabolomics research community: A 2017-2018 update

The scale at which MS- and NMR-based platforms generate metabolomics datasets for both research, core, and clinical facilities to address challenges in the various sciences-ranging from biomedical to agricultural-is underappreciated. Thus, metabolomics efforts spanning microbe, environment, plant, animal, and human systems have led to continual and concomitant growth of in silico resources for analysis and interpretation of these datasets. These software tools, resources, and databases drive the field forward to help keep pace with the amount of data being generated and the sophisticated and diverse analytical platforms that are being used to generate these metabolomics datasets. To address challenges in data preprocessing, metabolite annotation, statistical interrogation, visualization, interpretation, and integration, the metabolomics and informatics research community comes up with hundreds of tools every year. The purpose of the present review is to provide a brief and useful summary of more than 95 metabolomics tools, software, and databases that were either developed or significantly improved during 2017-2018. We hope to see this review help readers, developers, and researchers to obtain informed access to these thorough lists of resources for further improvisation, implementation, and application in due course of time.

Grape and Wine Metabolomics to Develop New Insights Using Untargeted and Targeted Approaches

Chemical analysis of grape juice and wine has been performed for over 50 years in a targeted manner to determine a limited number of compounds using Gas Chromatography, Mass-Spectrometry (GC-MS) and High Pressure Liquid Chromatography (HPLC). Therefore, it only allowed the determination of metabolites that are present in high concentration, including major sugars, amino acids and some important carboxylic acids. Thus, the roles of many significant but less concentrated metabolites during wine making process are still not known. This is where metabolomics shows its enormous potential, mainly because of its capability in analyzing over 1000 metabolites in a single run due to the recent advancements of high resolution and sensitive analytical instruments. Metabolomics has predominantly been adopted by many wine scientists as a hypothesis-generating tool in an unbiased and non-targeted way to address various issues, including characterization of geographical origin (terroir) and wine yeast metabolic traits, determination of biomarkers for aroma compounds, and the monitoring of growth developments of grape vines and grapes. The aim of this review is to explore the published literature that made use of both targeted and untargeted metabolomics to study grapes and wines and also the fermentation process. In addition, insights are also provided into many other possible avenues where metabolomics shows tremendous potential as a question-driven approach in grape and wine research.

Systems biology primer: the basic methods and approaches

Systems biology is an integrative discipline connecting the molecular components within a single biological scale and also among different scales (e.g. cells, tissues and organ systems) to physiological functions and organismal phenotypes through quantitative reasoning, computational models and high-throughput experimental technologies. Systems biology uses a wide range of quantitative experimental and computational methodologies to decode information flow from genes, proteins and other subcellular components of signaling, regulatory and functional pathways to control cell, tissue, organ and organismal level functions. The computational methods used in systems biology provide systems-level insights to understand interactions and dynamics at various scales, within cells, tissues, organs and organisms. In recent years, the systems biology framework has enabled research in quantitative and systems pharmacology and precision medicine for complex diseases. Here, we present a brief overview of current experimental and computational methods used in systems biology.