GC-MS Notes

Gas Chromatography-Mass Spectrometry (GC-MS)

Chromatography Definition

  • Separation of sample components by selective adsorption or partitioning between a mobile phase and a stationary phase.

GC-MS

  • Combines gas chromatography (GC) and mass spectrometry (MS) to identify substances.

Gas Chromatography (GC)

  • Separates components based on their volatilities.

  • Components are partitioned between a mobile gaseous phase (carrier gas like helium or nitrogen) and a liquid or solid stationary phase in a column.

Mass Spectrometry (MS)

  • Measures the mass-to-charge ratio of ions.

  • Sample is ionized, causing charged fragments.

  • Ions are separated based on their mass-to-charge ratio using electric or magnetic fields.

Industries Using GC

  • Chemical/Petrochemical, Clinical/Forensic, Consumer Products, Environmental, Food, Pharmaceutical.

Advantages of GC

  • Simple, cheap (can be automated), short analysis times, high accuracy, qualitative and quantitative analysis.

  • Applicable in % to ppb level.

Compounds Amenable to GC

  • Thermally stable.

  • Un-reactive and non-absorptive to the chromatographic system.

  • Volatile at temperatures below 350-400 °C.

  • Presence of polar groups reduces volatility.

Types of GC

  • Gas-liquid chromatography (GLC): gas mobile phase, liquid stationary phase.

  • Gas-solid chromatography (GSC): gas mobile phase, solid stationary phase.

GC Types

  • GSC: Stationary phase - Solids (alumina, silica, polymers, carbon…); Principle - Adsorption

  • GLC: Stationary phase - immobilized liquids (siloxanes, polyethylene glycols..); Principle: Partition

Components of GC-MS

  • Carrier gas (mobile phase).

  • Sample injection system.

  • Column (stationary phase).

  • Ion source.

  • Mass analyzer.

  • Detectors.

Principle of GC-MS

  • Separation of volatile components based on their distribution and partition coefficient between two phases.

  • Ratio of solubility of substance in between gaseous mobile phase and stationary liquid phase.

  • Components partitioned into gas are eluted first.

GC-MS: How it Works

  1. Sample injected and vaporized.

  2. Transported by inert gas (mobile phase).

  3. Separated by interaction with the column coating (stationary phase).

  4. Converted to charged ions in the ion source.

  5. Separated by mass-to-charge ratio (m/z) using a magnetic field.

Carrier Gas (Mobile Phase)

  • Transports analyte through the column.

  • Does not interact with analyte.

  • Flow quantified by linear velocity or volumetric flow rate.

  • Molecular sieve to remove water and impurities.

  • Common gases: Nitrogen, Helium, Hydrogen.

Carrier Gas Advantages/Disadvantages

  • Nitrogen: Cheap, readily available, Long run times

  • Helium: Good compromise, safe, Expensive

  • Hydrogen: Shorter run times, cheap, Explosive

Sample Injection System

  • Sample injected and vaporized into the column.

  • Injector is a heated, glass-lined cylinder.

  • Optimal column efficiency requires small, quick injections to prevent band broadening.

Injection Port

  • Sample loaded via hypodermic syringe.

  • Heated (350°C) to volatilize the sample.

  • Gas phase sample carried to mixing chamber before entering column.

  • Split injection system reduces sample volume via gas stream.

Injection Mode

  • Split Mode: small sample amount, concentrated sample, narrow peaks

  • Splitless Mode: most of the sample, low concentration samples, wider peaks

Column Types

  • Packed column.

  • Capillary column (open tubular).

Packed Column

  • Less common.

  • Glass or steel, 1 to 5 m length.

  • Internal diameter: 2 to 4 mm.

  • Packed with porous support coated with liquid stationary phase.

  • Advantages: Large sample size, ease of use.

Capillary Column

  • Widely used.

  • Length: 10 – 100 m.

  • Coiled around metallic support.

  • Types: FSOT, WCOT, SCOT.

  • Advantages: High resolution, short analysis time, high sensitivity.

Column Selection Parameters

  • Dimensions: internal diameter, column length, film thickness.

  • Conditions: temperature, flow rate.

  • Composition: stationary phase, carrier gas.

  • Stationary phase choice is critical for the sample to be run.

Factors Affecting GC Separations

  • Volatility of compound: Low b.p components travel faster.

  • Polarity of compounds: Polar compounds move more slowly.

  • Column temperature: Raising temperature speeds up all compounds.

  • Flow rate: Speeding up gas flow increases compound speed.

  • Column length: Longer column increases elution time.

Column Temperature

  • Increase in temperature gradient during separation, increase the solute vapor pressure and hence decrease the retention time

Column (Stationary Phase) Properties

  • Low volatility.

  • Thermal stability.

  • Chemical inertness.

  • Solvent characteristics.

Separation Principles

  • "Like dissolves like" based on polarity.

  • Polarity order:
    Aliphatic hydrocarbons < olefins < aromatic hydrocarbons < halides < ethers < esters/aldehydes/ketones < alcohols/amines < amides < carboxylic acids < water

  • Match stationary phase polarity to sample components; elution order determined by boiling point.

Stationary Phase Basics

  • "Choose a stationary phase that 'looks like' the components you want to separate."

Polarity of Stationary Phase

  • Polar: Water, Carboxylic acids, Amides, Alcohol/amines, Esters/aldehydes/ketones.

  • Non-polar: Ethers, Halides, Aromatic hydrocarbons, Olefins, Aliphatic hydrocarbons.

Stationary Phases

  • Polysiloxanes or polyethylene glycol (PEG) based.

  • PEG used for polar species.

  • Polydimethyl siloxane, the R groups are all CH3. (Non- polar)

Column Temperature Optimization

  • Dependent on sample's boiling point.

  • Minimal temperatures enhance resolution but increase elution times.

  • Temperature roughly ≥ the average boiling point yields reasonable elution.

Ion Source

  • Separated compounds are ionized.

  • Electrons ejected from sample molecules create positive ions.

  • Ionization methods: Electron impact (EI), Chemical ionization (CI), Field desorption (FD), Fast atom bombardment (FAB).

Mass Analyzer

  • Ions deflected by magnetic field based on mass and charge.

  • Lighter ions deflect more.

  • Ions with higher charges deflect more.

  • Mass/charge ratio (m/z) is key.

Detector

  • Ions neutralized on metal box release electrons.

  • Electron flow detected as electric current.

  • Current is amplified and recorded; more ions mean greater current.

Detectors

  • Mass Spectrometer and Fourier Transform Infrared Spectrometers: Identify compounds by comparing spectrum with library of spectra using a computer

  • Compare retention times between reference sample and unknown

  • Peak Area Concentration of Standard: Peak area increases proportional to concentration of standard if unknown/standard have the identical retention time  same compound

Type of detectors

  • Thermal conductivity detector

  • Flame ionisation detector: Useful for organic compounds, atmospheric and aqueous environmental samples. Sample is destroyed

GC Analysis

  • Order of elution (retention time) determined by volatility.

  • Volatility depends on polarity of the compound and between the stationary phase.

  • Polar compound = least volatile = most retained Polar compound = polar stationary phase = most retained

GC-MS Result

  • Consists of a chromatogram and a mass spectrum.

  • Number of peaks indicates the number of components.

  • Area under the peaks indicates the amount of a given component.

  • Retention times allow for component identification when coupled with MS.

GC-MS Output

  • Simplified "stick diagram" shows relative current produced by ions of varying mass/charge ratio.

  • Vertical scale indicates ion abundance.

Applications of GC-MS

  • Metabolite profiling, detection of lipophilic compounds, analysis of aromatic amines, identification of volatile components, pesticide analysis, environmental and forensic applications, detection of genetic metabolic disorders.

GC-MS Uses

  • Detection of illegal narcotics, sports anti-doping analysis.

Advantages of GC-MS

  • High resolution separation.

  • Suitable for low molecular weight hydrophobic compounds.

  • Volatile compounds can be directly analyzed.

  • Database availability.

  • Suitable for mixture analysis.

Limitations of GC-MS

  • Not suitable for non-volatile and thermo-unstable compounds.

  • Slow analyzing time.

  • Harsh ionization.

  • Limited number of molecules can be analyzed.

  • Only compounds with vapor pressures exceeding about 10^{-10} torr can be analyzed.

  • Determining positional substitution on aromatic rings is often difficult.

  • Isomeric compounds may be indistinguishable.