Metabolomics techniques Flashcards
What is LC-MS, and how is it used in metabolomics?
Liquid Chromatography-Mass Spectrometry (LC-MS) is a high-throughput analytical technique utilized for the separation, identification, and quantification of small molecules (metabolites) in biological samples. It integrates Liquid Chromatography (LC) for the physical separation of metabolites with Mass Spectrometry (MS) for their mass-based detection and characterization.
What is NMR?
NMR (Nuclear Magnetic Resonance) Spectroscopy detects metabolites by analyzing how atomic nuclei (mainly hydrogen or carbon) interact with a magnetic field.
Unlike LC-MS, NMR does not require ionization or destruction of the sample.
What is Tandem Mass Spectrometry (MS/MS)?
Tandem Mass Spectrometry (MS/MS) is an advanced MS technique that fragments ionised molecules in multiple stages to improve identification and structural analysis.
Steps for LC-MS?
1️⃣ Sample Preparation: Metabolites are extracted from biological matrices such as blood, urine, or tissue lysates using solvent-based extraction techniques.
2️⃣ Chromatographic Separation: The extracted metabolites are separated based on polarity, hydrophobicity, or charge using reversed-phase, hydrophilic interaction (HILIC), or ion-exchange chromatography.
3️⃣ Ionization: Metabolites are ionized using techniques such as Electrospray Ionization (ESI) or Atmospheric Pressure Chemical Ionization (APCI) to generate gas-phase ions for mass analysis.
4️⃣ Mass Spectrometric Detection & Analysis: The mass-to-charge ratio (m/z) of ionized metabolites is measured using single-stage (MS) or tandem mass spectrometry (MS/MS) to provide molecular identification and structural insights.
5️⃣ Data Processing & Metabolite Identification: Detected ion peaks are aligned and matched to metabolite databases (e.g., METLIN, HMDB, KEGG) based on their m/z values , retention times and fragmentation spectra.
Interpretation of LC-MS Data?
LC-MS data is interpreted using:
✔ Retention time & m/z ratio → Identify metabolites by matching to databases.
✔ Peak intensity → Reflects metabolite abundance for quantification and comparison.
Applications of LC-MS in Metabolomics?
✅ Untargeted Metabolomics: Comprehensive global profiling of metabolites to discover novel biomarkers or metabolic perturbations.
✅ Targeted Metabolomics: Quantitative analysis of specific metabolites (e.g., glucose, amino acids, lipid species) with predefined reference standards.
✅ Metabolic Pathway Analysis: Mapping metabolite alterations in biological pathways (e.g., TCA cycle, glycolysis, lipid metabolism) in disease models such as cancer and metabolic disorders.
What are some Key Steps in NMR-Based Metabolomics?
1️⃣ Sample preparation: Dissolve metabolites in deuterated solvent (D₂O, CDCl₃).
2️⃣ Magnetic resonance detection: Apply a strong magnetic field and measure radiofrequency signals emitted by atomic nuclei.
3️⃣ Fourier transform analysis: Converts raw data into an NMR spectrum.
4️⃣ Metabolite identification: Chemical shifts (measured in ppm) indicate specific metabolites.
Results Interpretation NMR?
Peak position (chemical shift in ppm): Identifies metabolite type.
Peak area (integration): Reflects metabolite concentration.
What is NMR best used for and what are some limitations?
✔ Best Used For:
✅ Non-destructive analysis – Allows metabolite study without destroying the sample.
✅ Absolute metabolite quantification – Unlike LC-MS, NMR provides direct concentration measurements.
✅ Studying metabolic pathways in biofluids (e.g., glucose, lactate, amino acids in blood).
✔ Limitations:
❌ Lower sensitivity than LC-MS – Cannot detect very low-abundance metabolites.
❌ Expensive instrumentation (requires a high-field NMR machine).
Key steps in MS/MS?
Tandem Mass Spectrometry (MS/MS) analyzes molecules by fragmenting a parent ion and detecting fragment ions, creating a unique fingerprint for identification.
🔬 Key Steps:
1️⃣ MS1 (First Mass Spectrometry) → Detects the molecular ion (parent ion, m/z) to determine molecular weight.
2️⃣ Collision-Induced Dissociation (CID) → The parent ion is fragmented by colliding with inert gas (argon, helium).
3️⃣ MS2 (Second Mass Spectrometry) → Detects fragment ions, producing a unique fragmentation pattern for molecule identification.
Results Interpretation in MS/MS?
MS1 spectrum (m/z of parent ion) → Determines the metabolite’s molecular weight.
MS2 fragmentation pattern → Identifies structural components.
What is MS/MS best used for and what are some limitations?
✔ Best Used For:
✅ Structural elucidation – Confirms metabolite identity by analyzing fragmentation patterns.
✅ High-precision quantification – Used in targeted metabolomics (e.g., drug metabolism studies).
✅ Detecting metabolic disease biomarkers (e.g., abnormal amino acid levels in metabolic disorders).
✔ Limitations:
❌ Sample ionization bias – Some metabolites ionize more efficiently than others.
❌ Data complexity – Requires specialized software for spectral matching.
