Understanding complex mixtures, retention‑time data
3. Basic Principle of a Mass Spectrometer
Ionisation – neutral molecules are converted into gas‑phase ions (radical cations or protonated species).
Mass‑to‑charge (m/z) separation – ions are separated according to their mass‑to‑charge ratio.
Detection – the separated ions are counted; an electrical signal is plotted as a mass spectrum.
The spectrum shows relative ion abundance (intensity) versus m/z. The highest‑mass peak that corresponds to the intact ion is the molecular ion (M⁺· for EI, [M+H]⁺ for soft ionisation).
4. Main Components of a Mass Spectrometer
Component
Function (Key Points for A‑Level)
Ion source
Generates gas‑phase ions. Common A‑Level sources: Electron Impact (EI) and Chemical Ionisation (CI). (FAB, MALDI, ESI are useful for context.)
Mass analyser
Separates ions by m/z. Main types:
Quadrupole – selects a single m/z at a time; resolution Δm/m ≈ 0.1 %.
Time‑of‑flight (TOF) – measures flight time; Δm/m as low as 0.02 % with reflectron.
Detector
Counts ions (electron multiplier, Faraday cup) and converts the count into a voltage for the spectrum.
Vacuum system
Maintains 10⁻⁵–10⁻⁶ Pa so ions travel without collisions; essential for all analysers.
4.1 Resolution & Accuracy
Resolution (Δm/m) – ability to distinguish two close m/z values. Higher resolution = sharper peaks, easier isotope discrimination.
Accuracy (ppm) – closeness of the measured m/z to the true value. Achieved by calibrating with known standards or internal reference ions.
5. Ionisation Methods Used at A‑Level
Electron Impact (EI) – 70 eV electrons remove an electron, giving a radical cation M⁺·. Extensive fragmentation; ideal for library matching.
Chemical Ionisation (CI) – a reagent gas (CH₄, NH₃, etc.) is first ionised; the reagent ion transfers a proton or attaches to the analyte, producing [M+H]⁺ or [M+CH₃]⁺. Much gentler fragmentation.
Fast Atom Bombardment (FAB) – neutral Ar atoms strike a matrix‑dissolved sample; mainly [M+H]⁺ with limited fragmentation (useful for polar, non‑volatile compounds).
MALDI – laser‑desorption from a solid matrix; ions appear as [M+H]⁺ or [M+Na]⁺ (common for biomolecules).
For the Cambridge A‑Level exam the focus is on EI and CI, but a brief awareness of FAB, MALDI and ESI helps students understand why different sources are chosen for different classes of compounds.
6. Interpreting a Mass Spectrum (Systematic Approach)
Locate the molecular ion peak (M⁺· or [M+H]⁺) – gives the molecular mass.
Apply the nitrogen rule – odd m/z ⇒ odd number of N atoms; even ⇒ 0 or even number of N atoms.
Examine isotopic patterns for Cl, Br, S (and for C/H isotopes in high‑resolution work).
Identify common neutral losses (H₂O 18 u, CO 28 u, CO₂ 44 u, CH₃ 15 u, C₂H₅ 29 u, etc.) and calculate the corresponding fragment m/z values.
Use fragmentation rules** to propose sub‑structures:
α‑cleavage – bond cleavage adjacent to a heteroatom or functional group.
β‑cleavage – loss of a fragment two bonds away (often gives alkyl cations).
McLafferty rearrangement – γ‑hydrogen transfer to a carbonyl oxygen, loss of 42 u (CH₂CO).
Other characteristic losses – e.g., loss of CH₃O (31 u) from esters.
Combine the information to write a plausible molecular formula and draw a structure.
6.1 Nitrogen Rule
If the molecular ion has an oddm/z, the molecule contains an odd number of nitrogen atoms. An evenm/z indicates zero or an even number of nitrogens.
6.2 Isotopic Patterns (Key Halogens)
Element
Isotopes (abundance)
Typical pattern in spectrum
Chlorine (Cl)
⁽³⁵⁾Cl 75 % / ⁽³⁷⁾Cl 25 %
M and M+2 peaks in a 3 : 1 intensity ratio
Bromine (Br)
⁽⁷⁹⁾Br 50 % / ⁽⁸¹⁾Br 50 %
M and M+2 peaks of almost equal intensity
Sulphur (S)
⁽³²⁾S 95 % / ⁽³⁴⁾S 4.2 %
Small M+2 satellite (~4 % of M)
6.3 Common Fragmentation Rules (A‑Level Focus)
α‑cleavage – bond break next to a heteroatom (e.g., –C–O–, –C–N–) giving M⁺· – R fragments.
β‑cleavage – loss of a β‑fragment, often producing stable alkyl cations such as C₂H₅⁺ (m/z = 29).
McLafferty rearrangement – γ‑hydrogen transfer to a carbonyl oxygen; characteristic loss of 42 u (CH₂CO).
Loss of small neutrals – H₂O (18 u), CO (28 u), CO₂ (44 u), CH₃ (15 u), C₂H₅ (29 u), etc.
7. Quantitative Use of Peak Intensities (AO3)
Peak intensity is proportional to the amount of ion reaching the detector, but the relationship is not absolute because ionisation efficiency varies between compounds.
To obtain quantitative data:
Prepare a series of standards of known concentration.
Record the intensity of a characteristic ion (usually the base peak or the molecular ion).
Plot intensity versus concentration to generate a calibration curve.
Analyse the unknown sample under identical conditions; read its concentration from the calibration curve.
Use an internal standard (a compound not present in the sample but with similar ionisation behaviour) to correct for variations in injection volume or source stability.
Report results with appropriate significant figures and, where required, the relative standard deviation (RSD).
8. Limitations & Practical Considerations
Volatility – EI and CI require the sample to be vapour‑phase; non‑volatile or thermally labile compounds need soft ionisation (FAB, MALDI, ESI).
Fragmentation – Extensive fragmentation (especially EI) can obscure the molecular ion, making formula determination difficult.
Vacuum requirement – High vacuum is essential; leaks or insufficient pumping degrade resolution and sensitivity.
Matrix effects – In FAB, MALDI and ESI the choice of matrix or solvent can suppress or enhance ion signals.
Safety – High voltages (up to 10 kV) and electron beams are hazardous; proper grounding and interlocks are mandatory.
Many A‑Level exam questions provide a library spectrum (or a set of reference peaks). The typical procedure is:
Identify the molecular ion in the unknown spectrum.
Compare the pattern of fragment peaks with the library entries.
Select the library spectrum that shows the same base peak, characteristic neutral losses and isotopic pattern.
Confirm the choice by checking that the calculated molecular formula matches the molecular ion mass.
Library matching is a quick way to identify an unknown when a suitable database is available.
10. Worked Example
Problem: The spectrum below shows the most intense peaks at m/z = 58 (M⁺·), 43, 30, 29 and 15. Determine a plausible molecular formula and propose a structure.
Molecular ion – M⁺· = 58 u.
Nitrogen rule – 58 is even ⇒ 0 or an even number of N atoms. For a simple organic molecule we assume 0 N.
Possible elemental combinations (using C, H, O, S):
C₄H₁₀O (4 × 12 + 10 × 1 + 16 = 58)
C₃H₆O₂ (3 × 12 + 6 × 1 + 2 × 16 = 58)
C₂H₂S₂ (2 × 12 + 2 × 1 + 2 × 32 = 58)
The simplest formula that fits the observed fragments is C₄H₁₀O.
Fragment analysis:
58 → 43 (loss of 15 u) ⇒ loss of a CH₃ group.
58 → 30 (loss of 28 u) ⇒ loss of CO, typical for an alcohol or aldehyde.
29 = C₂H₅⁺ (ethyl cation) – common from a carbon chain.
15 = CH₃⁺ (methyl cation).
Proposed structure – butan‑1‑ol, CH₃CH₂CH₂CH₂OH, fits C₄H₁₀O and explains the observed neutral losses (CH₃, CO, and the ethyl fragment).
Check‑Your‑Answer Tip
After you have selected a formula, verify it against any isotopic pattern (e.g., absence of a Cl/Br M+2 satellite) and confirm that the fragments can be generated by the rules listed in Section 6.3. If an alternative formula also fits the mass, see whether it predicts a fragment that is *not* observed – this helps eliminate wrong possibilities.
11. Summary Checklist (Exam‑Ready)
Locate the molecular ion (M⁺· or [M+H]⁺) – gives the molecular mass.
Apply the nitrogen rule to infer the presence of nitrogen.
Inspect isotopic patterns for Cl, Br, S (and for high‑resolution C/H if required).
Identify common neutral losses (H₂O, CO, CO₂, CH₃, C₂H₅, etc.).
Use fragmentation rules (α‑cleavage, β‑cleavage, McLafferty, etc.) to propose sub‑structures.
Combine mass, formula, and fragment information to write a plausible molecular formula and draw a structure.
For quantitative questions: remember calibration, internal standards and the linear relationship between intensity and concentration.
Be aware of practical limitations – volatility, fragmentation, vacuum, matrix effects and safety.
If a library spectrum is supplied, match the pattern of peaks before confirming the identity.
Suggested diagram: Schematic of a mass spectrometer showing the ion source, mass analyser (quadrupole, magnetic sector or TOF), detector and vacuum system.
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