Graduate
  1. Physical Chemistry  1.1. Thermodynamics  1.1.1. Laws of Thermodynamics  1.1.2. Enthalpy and heat capacity  1.1.3. Entropy and free energy  1.1.4. Phase Equilibrium  1.1.5. Statistical thermodynamics  1.1.6. Thermodynamic cycle  1.1.7. Fugacity and activity  1.2. Quantum Chemistry  1.2.1. Principles of quantum mechanics  1.2.2. Schrödinger Equation  1.2.3. Particle in a box  1.2.4. Operators and eigenvalues  1.2.5. Atomic orbitals  1.2.6. Molecular orbital theory  1.2.7. Perturbation theory  1.2.8. Valence bond theory  1.2.9. Hybridization and chemical bonding  1.3. Chemical kinetics  1.3.1. Rate laws and reaction mechanisms  1.3.2. Collision theory  1.3.3. Transition state theory  1.3.4. Enzyme Kinetics  1.3.5. Chain Reactions and Polymerization  1.3.6. Photochemical reactions  1.4. Statistical mechanics  1.4.1. Partitioning functions  1.4.2. Molecular distribution functions  1.4.3. Boltzmann Distribution  1.4.4. Bose–Einstein and Fermi–Dirac statistics  1.5. Spectroscopy  1.5.1. Rotational Spectroscopy  1.5.2. Vibrational Spectroscopy  1.5.3. Electronic Spectroscopy  1.5.4. Nuclear magnetic resonance spectroscopy  1.5.5. Mass Spectrometry  1.5.6. Raman Spectroscopy  1.5.7. Electron paramagnetic resonance spectroscopy  1.6. Surface and colloidal chemistry  1.6.1. Absorption isotherm  1.6.2. Surface tension and wetting  1.6.3. Colloidal Stability  1.6.4. Catalysis  1.6.5. Emulsions and micelles  1.7. Electrochemistry  1.7.1. Nernst equation  1.7.2. Electrochemical cells  1.7.3. Conductivity and mobility  1.7.4. War  1.7.5. Fuel cells  1.7.6. Electrolysis
  2. Organic chemistry  2.1. Reaction mechanism  2.1.1. Nucleophilic substitution reactions  2.1.2. Electrophilic addition reactions  2.1.3. Elimination reactions  2.1.4. Rearrangement reactions  2.1.5. Radical reactions  2.1.6. Pericyclic reactions  2.2. Spectroscopy and structural determination  2.2.1. UV-Vis Spectroscopy  2.2.2. IR Spectroscopy  2.2.3. NMR Spectroscopy  2.2.4. Mass Spectrometry  2.2.5. X-ray crystallography  2.3. Stereoscopic  2.3.1. Chirality and optical activity  2.3.2. Structural analysis  2.3.3. Geometrical isomerism  2.3.4. Dynamic Stereochemistry  2.4. Organometallic Chemistry  2.4.1. Organolithium and organomagnesium reagents  2.4.2. Palladium-catalyzed cross-coupling reactions  2.4.3. Transition Metal Complexes  2.4.4. Metal–carbon bond  2.5. Polymer chemistry  2.5.1. Polymerization mechanism  2.5.2. Polymer Characteristics  2.5.3. Biodegradable Polymer  2.5.4. Conducting polymer  2.5.5. Supramolecular polymers  2.6. Medicinal chemistry  2.6.1. Drug design and development  2.6.2. Pharmacokinetics and pharmacodynamics  2.6.3. Structure-activity relationships  2.6.4. Molecular docking and drug screening
  3. Inorganic chemistry  3.1. Coordination chemistry  3.1.1. Crystal field theory  3.1.2. Ligand field theory  3.1.3. Spectrochemical Series  3.1.4. Chelation and stability  3.2. Organometallic Chemistry  3.2.1. Metal Carbonyls  3.2.2. Catalysis by organometallic complexes  3.2.3. Metallocenes  3.3. Bio-inorganic chemistry  3.3.1. Metalloproteins and enzymes  3.3.2. The role of metals in biological systems  3.3.3. Metal ion transport and storage  3.4. Solid state chemistry  3.4.1. Crystal Structures  3.4.2. Band theory of solids  3.4.3. Superconductors  3.4.4. Defects in the crystal  3.5. Lanthanides and Actinides  3.5.1. Electronic configuration in lanthanides and actinides  3.5.2. Coordination chemistry of the lanthanides  3.5.3. Magnetic Properties of Lanthanides
  4. Analytical chemistry  4.1. Chromatography  4.1.1. Gas Chromatography  4.1.2. High Performance Liquid Chromatography  4.1.3. Thin Layer Chromatography  4.2. Spectroscopic Techniques  4.2.1. Atomic absorption spectroscopy  4.2.2. X-ray diffraction  4.2.3. Inductively coupled plasma spectroscopy  4.3. Electroanalytical methods  4.3.1. Potentiometry  4.3.2. Voltammetry  4.3.3. Colometry  4.4. Mass Spectrometry  4.4.1. Ionization Technique  4.4.2. Fragmentation Pattern  4.5. Chemometrics  4.5.1. Multidisciplinary analysis  4.5.2. Machine Learning in Chemistry
  5. Theoretical and Computational Chemistry  5.1. Molecular dynamics simulation  5.1.1. Force fields and energy minimization  5.1.2. Monte Carlo simulation in molecular dynamics simulations  5.2. Quantum chemical methods  5.2.1. Hartree–Fock theory  5.2.2. Density functional theory  5.2.3. Semi-empirical methods  5.3. Computational drug design  5.3.1. Molecular Docking  5.3.2. QSAR Modeling  5.3.3. Virtual Screening
  6. Biochemistry  6.1. Enzyme Kinetics  6.1.1. Michaelis-Menten kinetics  6.1.2. Inhibition mechanism  6.2. Metabolism and Bioenergetics  6.2.1. Glycolysis  6.2.2. Citric acid cycle  6.2.3. Electron transport chain  6.3. molecular Biology  6.3.1. DNA replication and repair  6.3.2. Protein synthesis  6.3.3. Gene Regulation  6.4. Structural Biochemistry  6.4.1. Protein Folding  6.4.2. Membrane Biophysics
  7. Environmental Chemistry  7.1. Atmospheric Chemistry  7.1.1. Greenhouse gases  7.1.2. Ozone depletion  7.1.3. Air pollutants and smoke  7.2. Water Chemistry  7.2.1. pH and water hardness  7.2.2. Wastewater treatment  7.2.3. Aquatic Chemistry  7.3. Soil Chemistry  7.3.1. Heavy metal contamination  7.3.2. Soil pH and Buffering  7.3.3. Nutrient cycling  7.4. Toxicology and Chemical Safety  7.4.1. Toxicokinetics  7.4.2. Risk Assessment in Toxicology and Chemical Safety in Environmental Chemistry  7.4.3. Effects of pollutants on the environment

Graduate → Analytical chemistry ↓


Mass Spectrometry


Mass spectrometry (MS) is an analytical technique used to measure the mass-to-charge ratio of ions. It has become a core technique in the field of analytical chemistry due to its ability to identify compounds with high specificity, sensitivity, and speed. This technique is invaluable for both qualitative and quantitative applications. Understanding the principles and applications of mass spectrometry is important for chemists and researchers across many scientific disciplines.

Fundamentals of mass spectrometry

The basic principle of mass spectrometry is to detect ions based on their mass-to-charge ratio (m/z). This is accomplished through several major steps:

  1. Ionization: Molecules are ionized, which means they are converted into ions, usually by losing or gaining electrons.
  2. Acceleration: Ions are accelerated in an electric field, so that all ions with the same charge have the same kinetic energy.
  3. Deflection: The ions are then deflected by the magnetic field. The degree of deflection depends on the mass and charge of the ions; lighter ions or ions with less charge are deflected more.
  4. Detection: The delocalized ions are detected, and the mass spectrometer records m/z values corresponding to the different ions.

Components of a mass spectrometer

A mass spectrometer has several major components, each of which plays a vital role in the operation of the instrument. These include:

1. Ion source

The ion source is responsible for converting the molecules of the sample into ions. Various ionization techniques are used, each of which is suitable for different types of samples:

  • Electron ionization (EI): Common for small and unstable compounds. Electrons are used to ionize molecules in the gas phase.
  • Chemical ionization (CI): Soft ionization technique that uses a reagent gas.
  • Matrix-assisted laser desorption/ionization (MALDI): This is useful for larger biomolecules such as proteins and polymers, using a laser and matrix to assist in ionization.
  • Electrospray ionization (ESI): Particularly useful for analyzing large biomolecules in solution by generating ions directly from the liquid phase.

2. Mass analyzer

The mass analyzer separates ions based on their m/z ratio. Some of the widely used types of mass analyzers are:

  • Quadrupole mass analyzer: uses an oscillating electric field to filter out ions of specific m/z values.
  • Time-of-flight (TOF) mass analyzer: measures the time it takes for ions to travel a certain distance, allowing their m/z ratio to be calculated.
  • Ion trap mass analyzer: Traps ions in a certain area using electric and magnetic fields, then releases and detects them.
  • Fourier transform ion cyclotron resonance (FTICR) mass analyzer: An advanced technique that uses a magnetic field to charge-trap ions, measuring frequencies related to m/z.

3. Detector

Detectors are the final components that register the incoming ions and convert it into a signal that can be recorded and analyzed. These include:

  • Electron multiplier: Amplifies the ion signal by creating a cascade of electrons.
  • Faraday cup: Collects ions to produce an electric current, which is directly related to the number of ions.
  • Microchannel plate detector: Suitable for sensitive applications, uses many small channels to amplify incoming ion signals.

Visual example: mass spectrometer design

Sample Introduction Ion Source Mass Analyzer Detectors

Applications of mass spectrometry

Mass spectrometry is used in a wide variety of applications in many fields, such as:

  • Proteomics: the identification and quantification of proteins in biological samples.
  • Metabolomics: Determining metabolic profiles and pathways in cells and tissues.
  • Environmental analysis: Detection of pollutants and contaminants in environmental samples.
  • Pharmaceuticals: drug discovery and development through analysis of drug interactions and degradation.
  • Forensics: Determining substances such as toxins or explosive residues at crime scenes.

Lesson example: real world application

In pharmaceutical research, mass spectrometry is important for the analysis of complex mixtures and the identification of drug metabolites.
For example, an unknown compound can be identified from its mass spectrum, because the mass and fragmentation pattern provide a "fingerprint" for it.
compounds. This has been helpful in speeding up the drug discovery process.

Interpretation of mass spectra

Interpreting mass spectra involves understanding m/z values, peak patterns, and relative intensities. Common types of information obtained from mass spectra include:

  • Base peak: The most intense peak in the spectrum, representing the ion present in the highest amount.
  • Molecular ion peak (M+): Represents the ion corresponding to the entire molecule, usually appearing as the peak with the highest m/z value.
  • Fragment ions: Formed by the breaking up of a molecular ion into smaller pieces, providing information about the structure and bonding of the molecule.

Visual example: simplified mass spectrum

50 100 150 M+ Fragment ions

Advances in mass spectrometry

Rapid developments in the field of mass spectrometry have greatly expanded its capabilities and applications. Some notable advances include:

  • High-resolution mass spectrometry (HRMS): Provides the precise mass measurements needed to resolve isobaric species and elucidate complex structures.
  • Tandem mass spectrometry (MS/MS): This involves multiple steps of mass spectrometry for detailed structural elucidation and increased specificity in compound identification.
  • Imaging mass spectrometry: Provides spatial distribution maps of molecules in biological tissues, allowing localization studies at molecular levels.
  • Ambient mass spectrometry: allows for the direct analysis of samples in their natural state, reducing sample preparation steps.

Mass spectrometry remains an indispensable tool in analytical chemistry, with ongoing innovations promising further refinement and wider applicability across scientific fields. Its versatility and accuracy in identifying and quantifying molecules contribute significantly to advances in research, diagnostics, drug development, and many other fields.


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Mass Spectrometry

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