Podcast
Questions and Answers
Metabolomics is best described as the study of:
Metabolomics is best described as the study of:
- Proteins and their functions within biological systems.
- RNA molecules in a cell and their expression.
- The complete set of genes in a cell or organism.
- Small molecule metabolites and their interactions in biological systems. (correct)
Genomics directly reflects the current physiological state of a cell at a given moment.
Genomics directly reflects the current physiological state of a cell at a given moment.
False (B)
Define phenotype in the context of molecular biology and explain why metabolomics is considered closely related to it.
Define phenotype in the context of molecular biology and explain why metabolomics is considered closely related to it.
Phenotype refers to the observable characteristics of an organism resulting from the interaction of its genotype with the environment. Metabolomics is closely related because it directly measures the small molecules that are the end products of cellular processes, reflecting the functional state of the cell or organism at a given time.
The process of converting DNA into RNA is known as ______, while the process of converting RNA into protein is known as ______.
The process of converting DNA into RNA is known as ______, while the process of converting RNA into protein is known as ______.
Match each 'omics' field with what it primarily reflects:
Match each 'omics' field with what it primarily reflects:
Which of the following is NOT a post-translational modification (PTM)?
Which of the following is NOT a post-translational modification (PTM)?
Western blotting is a technique used to primarily analyze metabolite levels in a sample.
Western blotting is a technique used to primarily analyze metabolite levels in a sample.
Explain the role of cell signaling in biological systems and list two types of signals that cells can respond to.
Explain the role of cell signaling in biological systems and list two types of signals that cells can respond to.
The Warburg effect in cancer cells describes their preference for ______ over oxidative phosphorylation, even in the presence of oxygen.
The Warburg effect in cancer cells describes their preference for ______ over oxidative phosphorylation, even in the presence of oxygen.
In the context of metabolomics, 'flux analysis' using 13C isotopes is used to:
In the context of metabolomics, 'flux analysis' using 13C isotopes is used to:
Mass spectrometry (MS) is a technique that directly measures the mass-to-charge ratio (m/z) of ions.
Mass spectrometry (MS) is a technique that directly measures the mass-to-charge ratio (m/z) of ions.
Differentiate between targeted and untargeted metabolomics approaches in terms of their objectives and scope.
Differentiate between targeted and untargeted metabolomics approaches in terms of their objectives and scope.
In mass spectrometry, ______ chromatography is often coupled with MS for separation of complex mixtures before metabolite detection.
In mass spectrometry, ______ chromatography is often coupled with MS for separation of complex mixtures before metabolite detection.
Which of the following is an advantage of Nuclear Magnetic Resonance (NMR) spectroscopy in metabolomics compared to Mass Spectrometry (MS)?
Which of the following is an advantage of Nuclear Magnetic Resonance (NMR) spectroscopy in metabolomics compared to Mass Spectrometry (MS)?
Gas Chromatography-Mass Spectrometry (GC-MS) is generally more suitable for analyzing polar metabolites without derivatization compared to Liquid Chromatography-Mass Spectrometry (LC-MS).
Gas Chromatography-Mass Spectrometry (GC-MS) is generally more suitable for analyzing polar metabolites without derivatization compared to Liquid Chromatography-Mass Spectrometry (LC-MS).
Describe the basic principle of chromatography in the context of metabolomics sample analysis.
Describe the basic principle of chromatography in the context of metabolomics sample analysis.
In reversed-phase HPLC, a ______ stationary phase is used, which is effective for separating ______ compounds.
In reversed-phase HPLC, a ______ stationary phase is used, which is effective for separating ______ compounds.
Electrospray ionization (ESI) is a common ionization technique in mass spectrometry, particularly useful for:
Electrospray ionization (ESI) is a common ionization technique in mass spectrometry, particularly useful for:
Time-of-Flight (TOF) mass analyzers are known for their high mass resolution and mass accuracy.
Time-of-Flight (TOF) mass analyzers are known for their high mass resolution and mass accuracy.
What is the purpose of 'data processing' in metabolomics workflows, and name one common step involved.
What is the purpose of 'data processing' in metabolomics workflows, and name one common step involved.
[Blank] is a multi-variant statistical method commonly used in metabolomics data analysis for dimensionality reduction and visualization of group differences.
[Blank] is a multi-variant statistical method commonly used in metabolomics data analysis for dimensionality reduction and visualization of group differences.
The SCIO device utilizes which type of spectroscopy for metabolite analysis?
The SCIO device utilizes which type of spectroscopy for metabolite analysis?
Metabolomics is primarily used in isolation and has limited integration with other 'omics' fields like genomics and proteomics.
Metabolomics is primarily used in isolation and has limited integration with other 'omics' fields like genomics and proteomics.
Explain how metabolomics can be applied in cancer research for biomarker discovery and targeted therapy development.
Explain how metabolomics can be applied in cancer research for biomarker discovery and targeted therapy development.
The Kyoto Encyclopedia of Genes and Genomes (KEGG) and HMDB (Human Metabolome Database) are examples of ______ used in metabolomics for pathway analysis and metabolite identification.
The Kyoto Encyclopedia of Genes and Genomes (KEGG) and HMDB (Human Metabolome Database) are examples of ______ used in metabolomics for pathway analysis and metabolite identification.
Which of the following is NOT a typical application of metabolomics?
Which of the following is NOT a typical application of metabolomics?
Metabolomics data analysis rarely utilizes machine learning and AI techniques.
Metabolomics data analysis rarely utilizes machine learning and AI techniques.
Match the chromatographic method with its typical application in metabolomics:
Match the chromatographic method with its typical application in metabolomics:
Which statement is TRUE regarding the sensitivity and accuracy of LC-MS compared to spectroscopic tools like NMR?
Which statement is TRUE regarding the sensitivity and accuracy of LC-MS compared to spectroscopic tools like NMR?
Sample preparation is generally not required for metabolomics analysis using mass spectrometry.
Sample preparation is generally not required for metabolomics analysis using mass spectrometry.
Outline the general workflow of a metabolomics study, from biological question to biomarker validation.
Outline the general workflow of a metabolomics study, from biological question to biomarker validation.
In mass spectrometry, the ______ is responsible for separating ions based on their mass-to-charge ratio.
In mass spectrometry, the ______ is responsible for separating ions based on their mass-to-charge ratio.
Which of these factors is LEAST likely to be a 'driving process' in the Warburg effect?
Which of these factors is LEAST likely to be a 'driving process' in the Warburg effect?
The term 'metabolome' refers to the complete set of proteins in a biological system.
The term 'metabolome' refers to the complete set of proteins in a biological system.
What are 'take home notes' regarding definition of metabolomics?
What are 'take home notes' regarding definition of metabolomics?
Metabolic pathways are studied using targeted and ______ workflows in metabolomics.
Metabolic pathways are studied using targeted and ______ workflows in metabolomics.
Tools for metabolomics testing include:
Tools for metabolomics testing include:
Applications for metabolomics are limited to academic research and not relevant to industrial applications.
Applications for metabolomics are limited to academic research and not relevant to industrial applications.
Give examples of applications for metabolomics.
Give examples of applications for metabolomics.
Metabolomics focuses on the relative relationship between metabolites and ______ changes.
Metabolomics focuses on the relative relationship between metabolites and ______ changes.
The molecular weight range of small molecule metabolites typically studied in metabolomics is:
The molecular weight range of small molecule metabolites typically studied in metabolomics is:
Which 'omics' approach is considered to most accurately reflect the immediate physiological state of a biological system?
Which 'omics' approach is considered to most accurately reflect the immediate physiological state of a biological system?
Proteomics directly reflects what will happen in a biological system in response to a stimulus.
Proteomics directly reflects what will happen in a biological system in response to a stimulus.
Define metabolomics in terms of molecular weight and biological system changes.
Define metabolomics in terms of molecular weight and biological system changes.
The process of converting mRNA into a protein is known as ______.
The process of converting mRNA into a protein is known as ______.
Match the 'omics' approach with its description:
Match the 'omics' approach with its description:
Western blotting is a technique primarily used to analyze which biomolecules?
Western blotting is a technique primarily used to analyze which biomolecules?
Post-translational modifications (PTMs) increase the diversity and complexity of the proteome.
Post-translational modifications (PTMs) increase the diversity and complexity of the proteome.
Cell signaling primarily involves which of the following processes?
Cell signaling primarily involves which of the following processes?
Name two major analytical platforms commonly used in metabolomics.
Name two major analytical platforms commonly used in metabolomics.
In mass spectrometry, the separation of molecules is often achieved using chromatography, with ______ chromatography being particularly suited for polar compounds.
In mass spectrometry, the separation of molecules is often achieved using chromatography, with ______ chromatography being particularly suited for polar compounds.
Which of the following is a characteristic of targeted metabolomics?
Which of the following is a characteristic of targeted metabolomics?
Non-targeted metabolomics is typically used when reference standards for metabolites are readily available.
Non-targeted metabolomics is typically used when reference standards for metabolites are readily available.
The Warburg effect in cancer cells is characterized by:
The Warburg effect in cancer cells is characterized by:
What is the primary measurement obtained from Mass Spectrometry that is crucial for metabolite identification?
What is the primary measurement obtained from Mass Spectrometry that is crucial for metabolite identification?
In chromatography, the ______ phase is the stationary component that interacts with the analytes, leading to their separation.
In chromatography, the ______ phase is the stationary component that interacts with the analytes, leading to their separation.
Flashcards
What is Metabolomics?
What is Metabolomics?
Focuses on the relationship between metabolites and changes by examining the composition of small molecule metabolites in a biological system before and after stimulus during a specific period.
What is Phenotype?
What is Phenotype?
Molecules such as RNA and proteins. Most molecules and structures coded by the genetic material are not visible in the appearance of an organism, yet they are observable.
What is IDH?
What is IDH?
Isocitrate dehydrogenase catalyzes the oxidative decarboxylation of isocitrate, producing α-ketoglutarate and CO₂.
What Determines the Phenotype?
What Determines the Phenotype?
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What is Cell Signalling?
What is Cell Signalling?
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What is Warburg Effect?
What is Warburg Effect?
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What is 13C Metabolic Flux Analysis?
What is 13C Metabolic Flux Analysis?
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Metabolomics Workflow?
Metabolomics Workflow?
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What is Untargeted Metabolomics?
What is Untargeted Metabolomics?
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What is Targeted Metabolomics?
What is Targeted Metabolomics?
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What is Mass Spectrometry?
What is Mass Spectrometry?
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Parts of a Mass Spectrometer?
Parts of a Mass Spectrometer?
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What is NMR spectroscopy?
What is NMR spectroscopy?
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Column Chromatography?
Column Chromatography?
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What is Normal Phase?
What is Normal Phase?
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Reversed phase?
Reversed phase?
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What is Electrospray Ionization?
What is Electrospray Ionization?
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What is Time of Flight?
What is Time of Flight?
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LC-MS True Properties?
LC-MS True Properties?
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Study Notes
Introduction to Metabolomics
- Prepared by Dr Di Wu at Queen's University of Belfast.
Key Questions in Metabolomics
- What defines metabolomics?
- Why is it important to test metabolites?
- What tools are essential for metabolomics studies?
- What are the current and future applications?
Learning Outcomes
- Understanding the definition
- Recognizing metabolic pathways
- Identifying key tools for testing
- Exploring a range of applications
Defining Metabolomics
- Focuses on relative relationships between metabolites and changes in physiology and pathology.
- Examines the composition/content of small molecule metabolites with a molecular weight less than 1500 Da.
- Conducted in biological systems
- Monitors before and after stimulus or perturbation within a specific time frame.
- Genomics reflects potential occurrences, transcriptomics reflects what is going to happen.
- Proteomics indicates ongoing processes, while metabolomics reflects what has occurred.
- Metabolomics provides the closest insight into the biological phenotype.
Genotype to Phenotype at a Molecular Level
- Phenotype can depend on the genotype.
- RNA and proteins are included as molecules.
- Molecules coded by genetic material aren't always visible but are observable; Western blotting detects them.
- Observable characteristics or traits are made visible through technical procedures.
Gene Expressions
- Uses the genetic code to go from DNA to proteins
- mRNA is translated into a protein
Transcription Control
- Transcription: RNA polymerase synthesizes RNA using DNA as a template
- Is controlled by activators and repressors
Western Blots
- Used to determine protein level.
Post Translational Modifications (PTMs)
- Protein structures can be modified after translation
Cell Signaling Pathways
- Cell signaling is the ability of a cell to receive, process, and transmit signals with its environment and itself.
- Plays a fundamental role in prokaryotes and eukaryotes.
- Originating signals are physical agents like mechanical pressure, voltage, temperature, and chemical signals.
- Signalling occurs over short or long distances, in forms like autocrine, juxtacrine, intracrine, paracrine, or endocrine.
- Signalling molecules are synthesized from biosynthetic pathways or released through transports, or potentially even cell damage.
Isocitrate Dehydrogenase
- IDH1(Gene) is an enzyme
Metabolic Pathways
- Encompass carbohydrate, nucleotide, protein, and vitamin/cofactor metabolism.
- Includes the urea and citric acid cycles, cellular respiration, fatty acid, steroid, and lipid
Glycolysis
- Cytoplasmic process.
- Glucose is converted into pyruvate, generating a net gain of 2 ATP and 2 NADH molecules.
Citric Acid Cycle
- Krebs Cycle in mitochondria
- Acetyl-CoA is oxidized, producing ATP, NADH, and FADH2.
Warburg Effect
- Cancer cells show increased glucose uptake and glycolysis, even under normal oxygen conditions.
High-Resolution 13C Metabolic Flux Analysis
- Monitors the fate of carbon-13 labeled metabolites to trace metabolic pathways.
Achieving Metabolite Detection
- Requires appropriate tools and techniques.
Cancer Metabolism
- Early cancer metabolism events were mass spectrometry in 1931, Warburg winning Nobel Prize, NMR in 1947
General Workflow for Metabolomics
- Begins with a biological question/hypothesis, progressing through study design.
- Sample preparation, untargeted/targeted metabolomics, and NMR/MS-based platforms.
- Data processing, metabolite extraction, statistical evaluation, and data interpretation.
- Ends with biomarker validation and translation to clinical practice.
Targeted vs Non-Targeted Analysis
- Targeted focuses on specific metabolites, while non-targeted does broad spectrum analysis.
Untargeted and Targeted Metabolomics
| Untargeted Metabolomics | Targeted Metabolomics | |
|---|---|---|
| Characteristics | Comprehensive analysis of the entire metabolome; comparison of metabolite dynamics before/after stimulation; differential metabolites via bioinformatics/pathway analysis | For a substance or metabolite class; reference standards available; quantitative determination of target metabolite concentration |
| Purpose | Finding differences between sample groups, relative quantification. | Validating differences with focus on a metabolite or class, absolute quantification. |
Comparing Targeted and Non-Targeted MS
| Targeted MS-Metabolomics | Non-Targeted MS-Metabolomics |
|---|---|
| Identifies metabolites of interest | |
| Calibrates MS detection | Extracts |
| Extracts | Detects |
| Detects | Annotates and Reduces Statistically |
| Interprets | Interprets |
Nuclear Magnetic Resonance (NMR) Spectroscopy
- NMR applications in metabolomics can be viewed in a video.
Challenges in Metabolite Analysis
- The sensitivity of Nuclear Magnetic Resonance to Mass Spectrometry
Mass Spectrometry (MS)
- MS consists of separation techniques (LC, GC) and MS analysis.
- MS analysis involves mass spectrometry for detection and data acquisition.
- Includes high-resolution (Time of Flight, Orbitrap) and low-resolution (single, triple quadrupole).
Steps to Metabolite Identification
- Sample preparation, separation, ion sources, analyzers, and metabolite identification
Chromatography
- Involves color writing
- Uses a stationary and mobile phase, and a sample to pass over.
- The science and practice of pharmacy
Conventional Stationary Phases
- Varied types categorized by protection.
Compound Polarity and Solvents
- Solvents are rated by polarity as highly polar or non-polar
HPLC Column
- HPLC Columns are of reversed or normal phase for non or polar compounds
Electronic Spray Ion(ESI/EI) Source
- Applies an electronic spray
Time of Flight (ToF)
- A method of mass spectrometry.
- Remember that the MS only measures the m/z ratio of the ions
Data Processing
- Multi-variant analysis workflows
Metabolomics
- Metabolite extraction, untargeted LC/MS, metabolomics and then metabolic pathway mapping
Biomarker and Metabolic Target Identification
- Integrates multi-omics, uses single-cell and spatial detection, and applies novel analytics/experiments to improve detection.
- Precisely tracks metabolic rewiring.
- Offers personalized metabolic therapy.
Metabolomics Applications
- Single metabolite analysis from 1700s-2000
- Metabolomics and systems biology from 2000-present
- Organismal Level Deconvolution from 2010-present
SCIO and NIR
- Near-infrared spectroscopy
- SCIO Workflow and Spectrum used in sensing models
SCIO Black Tea
- SCIO NIR models for black tea samples show different areas, like Burundi, Ethiopia, and Malawi
FT-IR Black Tea
- Tea models using FT-IR of black tea can be determined
Artificial Intelligence
- AI-assisted data analysis using machine learning
Advantages and Disadvantages of Spectrometry and Mass Spectrometry
- In terms of speed, accuracy, cost, sensitivity, sample preparation and reproducibility
Future of Metabolomics
- Involves advanced instruments, databases/software, and methods development.
- Also emphasizes applications in biomedicine and drug discovery.
Take Home Notes
- Definition, metabolic pathways, tools like NMR, LC-MS, spectroscopic and applications.
- Consider 13C Metabolic Flux, Heatmap, regression, and biomarker identification.
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