lecture 4- mass spectrometry

MS

separation of charged gas phase ions according to mass to charge ratio

why is MS useful

• Target Identification: Confirms the presence of specific analytes.

• Universal Detector: Detects a wide range of compounds.

• High Sensitivity: Can detect very low concentrations.

• Molecular Mass & Structure: Provides molecular weight and clues about the structure of the analyte.

2 golden rules in MS

- requires production of gas-phase ions

- molecule can only be detected if it carries a charge

commonly used mass analysers

- magnetic sector MS

- quadrupole MS

magnetic sector MS

• Molecules from the sample are ionised

• Ions are accelerated by an electric field, giving all ions the same kinetic energy

• uncharged species collide with the walls and are pumped away by a vacuum system.

• Ions enter magnetic field and are deflected based on mass-to-charge ratio (m/z).

• Separated ions reach the detector for analysis.

quadrupole MS

• Molecules are ionised

• Ions pass between four parallel metal rods.

• Combination of RF (radio frequency) and DC (direct current) voltages create oscillating electric fields.

• Only ions with a specific mass-to-charge ratio (m/z) have stable paths and reach the detector.

• Other ions become unstable and crash into the rods.

• Scans m/z range by adjusting voltages.

what do you get from an MS

• Molecular Ion Peak (M⁺) → Represents the intact molecule, helps identify molecular weight.

• Fragmentation Pattern → The molecule breaks apart in predictable ways, giving clues about structure.

• Base peak: The most intense peak, representing the most abundant fragment.

• Mass-to-Charge Ratio (m/z) → Each peak corresponds to ions with specific m/z values.

• Relative Abundance → Shows how intense each ion is compared to the most intense peak (base peak).

• Qualitative Information → Helps identify unknown compounds.

• Quantitative Information → Can measure how much of a compound is present (especially with standards).

EI source: electron-neutral interaction

• A heated filament emits a beam of High-energy electrons (usually 70 eV)

• These collide with neutral gas-phase molecules.

• An electron is knocked out, forming a positive molecular ion (M⁺).

• The ionization energy of most organic molecules is 8–12 eV — 70 eV provides excess energy, causing fragmentation.

• Produces fragmentation patterns for mass analysis.

• Occasionally, negative ionization can also occur.

types of fragmentation

- heterolytic cleavage (halogens, ethers, alcohols)

- homolytic cleavage (halogens, ethers, alcohols, ketones)

- McLafferty rearrangements (e.g. ketones)

cleavages

- homolytic= electron pairs split evenly between atoms

- heterolytic= electron pairs split unevenly between atoms

nitrogen rule

Organic compounds containing H, C, N, O have:

• Odd molecular ion mass = odd number of nitrogen (N) atoms.

• Even molecular ion mass = no nitrogen (N) atoms, or even number of nitrogen atoms.

aliphatic hydrocarbons

• Linear, Saturated Alkanes: These molecules consist of carbon chains with single bonds (C-C).

• Weak C-C Bonds: The bonds between carbon atoms are relatively weak, leading to fragmentation at these points.

• Low Intensity M⁺ Ion: The molecular ion (M⁺) typically has low intensity compared to the fragments, as the molecule tends to fragment easily.

fragmentation characteristics

• Strong Molecules:

  • Less fragmentation.

  • Larger molecular ion (M⁺) peak.

  • These molecules are more stable and tend to remain intact during ionization.

• Weak Molecules:

  • More fragmentation.

  • Smaller molecular ion (M⁺) peak.

  • These molecules have weaker bonds and break apart more easily, producing numerous fragment ions.