Year 12 Chemistry Module 8 ⏱ ~35 min 5 MC · 3 Short Answer Lesson 12 of 16

Mass Spectrometry

Smash a molecule into charged pieces, weigh every fragment, and the pattern of masses becomes a fingerprint, telling you the molecule's mass and clues to how it was built. Mass spectrometry gives the molecular mass that anchors the whole structure-determination workflow.

Today's hook: A spectrum shows a peak at m/z = 64 and a second peak at m/z = 66 that is about one-third as tall, plus a tall peak at m/z = 49. Without ever seeing the molecule, a chemist reads off its mass, spots a chlorine atom from the two-peak pattern, and works out a fragment, all from a bar chart. How can the spacing and height of peaks reveal both an element and a piece of the structure?
0/5TASKS
Before you read

A mass spectrum shows its highest significant peak at m/z = 46, with a tiny peak just above it at m/z = 47.

  • What does the m/z = 46 peak most likely tell you about the molecule?
  • Why should you be careful about the small peak at m/z = 47, what could it be?
Learning Intentions

Know

  • What a mass spectrum shows (relative abundance vs m/z)
  • The meaning of the molecular ion (M⁺) peak and the base peak

Understand

  • How a molecule is ionised and fragmented, and why fragments appear at characteristic m/z
  • How isotope patterns reveal Cl, Br and C

Can Do

  • Read the molecular mass from the M⁺ peak and calculate the mass lost in a fragmentation
  • Use isotope peak ratios to detect chlorine and bromine
Key Terms
Mass-to-charge ratio (m/z)The x-axis of a mass spectrum; for singly charged ions (z = 1) it equals the ion's mass.
Molecular ion (M⁺)The radical cation formed when the intact molecule loses one electron; its m/z gives the molecule's molecular mass.
Base peakThe tallest peak (relative abundance 100%), the most abundant, most stable cation fragment (not always M⁺).
FragmentationBreaking of the molecular ion into a smaller cation (detected) plus a neutral radical (not detected).
Isotope patternExtra peaks (e.g. M+2) caused by heavier isotopes such as ³⁷Cl and ⁸¹Br.
M+1 peakA small peak one unit above M⁺, from molecules containing a ¹³C atom.
Where this fits: the qualitative tests in Lesson 11 tell you which functional group is present. Mass spectrometry is the first of three instrumental techniques (with IR in Lesson 13 and NMR in Lesson 14) that together determine a full structure, the capstone skill in Lesson 15. MS supplies the molecular mass that anchors the whole workflow.

Core Content

1

How a Mass Spectrometer Works

+5 XP

Five stages from sample to spectrum

A mass spectrometer separates charged particles by their mass-to-charge ratio in five stages:

  1. Vaporisation the sample is vaporised.
  2. Ionisation high-energy electrons knock an electron off each molecule, forming the molecular ion (a radical cation): M(g) → M⁺(g) + e⁻.
  3. Acceleration the positive ions are accelerated by an electric field.
  4. Deflection a magnetic field deflects ions by m/z (lighter or more highly charged ions deflect more).
  5. Detection a detector records the relative abundance at each m/z, producing the spectrum.

Only positively charged species reach the detector; the neutral radicals formed in fragmentation are not detected.

Five stages: vaporisation → ionisation (M → M⁺ + e⁻) → acceleration → deflection (by m/z) → detection. Only positive ions are detected; neutral fragments are not.

Pause, copy the highlighted five stages into your book.

Key idea: the magnetic field sorts ions by m/z, so the x-axis of every spectrum is mass-to-charge ratio, not time or wavelength.
Tap the stage in which a molecule first becomes a positive ion.
2

Reading the Molecular Ion → Molecular Mass

+5 XP

The peak at the highest mass usually gives the molecular mass

We just saw how a spectrometer produces peaks at different m/z. That raises a question: which peak tells you the molecule's mass? This card answers it → the molecular ion, normally the peak at the highest significant m/z.

The M⁺ peak is normally the peak at the highest m/z (ignoring small isotope peaks); its m/z equals the molecular mass, because the lost electron's mass is negligible.

1
Given: a spectrum's highest significant peak is at m/z = 46, with a formula consistent with C, H and O.
2
Find: the compound's molecular mass and a likely identity.
3
Method: molecular mass = M⁺ = 46. For C₂H₆O: 2(12) + 6(1) + 16 = 46.
4
Answer: molecular mass 46, consistent with ethanol, C₂H₅OH.

M⁺ = peak at the highest significant m/z = molecular mass. Watch the M+1 trap: a tiny peak one unit above is a ¹³C-containing molecule, not the molecular ion, choose the larger peak below it as M⁺.

Pause, copy the highlighted M⁺ rule into your book.

Common error: picking the small M+1 isotope peak as the molecular ion. The molecular ion is the larger peak just below it.
The m/z value of the molecular ion peak is equal to the:
3

Fragmentation & the Base Peak

+5 XP

Mass gaps between peaks reveal the pieces lost

We just saw that M⁺ gives the molecular mass. That raises a question: what do the smaller peaks mean? This card answers it → they are fragment cations, and the mass gaps between peaks reveal the neutral pieces lost.

After ionisation, many M⁺ ions break apart. A bond breaks to give a cation (detected, shows as a peak) plus a neutral radical (not detected). Fragmentation that forms a more stable carbocation is favoured (tertiary > secondary > primary).

The mass difference between two peaks tells you the neutral fragment lost. Common losses include: 15 = CH₃, 17 = OH, 29 = CHO or C₂H₅, 45 = COOH.

Worked example (loss of 15): pentane and 2-methylbutane both have M⁺ at m/z = 72. Both show a peak at m/z = 57 (72 − 15, loss of CH₃). The relative height at 57 differs because 2-methylbutane loses CH₃ to form a more stable secondary carbocation, so its 57 peak is comparatively larger.

The base peak (100% abundance) is the most stable, most abundant fragment cation, often not the molecular ion.

Mass gap between peaks = neutral fragment lost (15 = CH₃, 17 = OH, 29 = CHO/C₂H₅, 45 = COOH). Fragmentation favours the more stable cation. The base peak is the tallest peak (most abundant cation), often not M⁺.

Pause, copy the highlighted fragmentation rules into your book.

A molecule has M⁺ at m/z = 72 and a strong peak at m/z = 57. The neutral fragment lost is:
4

Isotope Patterns: Detecting Cl, Br and C

+5 XP

A second peak two units up can name an element

We just saw how mass gaps reveal fragments. That raises a question: can the spectrum also name specific elements? This card answers it → yes, characteristic isotope ratios flag chlorine, bromine and carbon.

  • Chlorine: ³⁵Cl : ³⁷Cl ≈ 3 : 1. One Cl gives M and M+2 peaks in roughly a 3 : 1 ratio.
  • Bromine: ⁷⁹Br : ⁸¹Br ≈ 1 : 1. One Br gives M and M+2 peaks of roughly equal height.
  • Carbon: about 1.1% of carbon is ¹³C, giving a small M+1 peak, the more carbons, the taller the M+1 peak relative to M⁺ (a rough carbon indicator).
  • Nitrogen rule: an odd M⁺ m/z usually means an odd number of nitrogen atoms.

Worked example, a chlorine-containing compound

1
Given: M⁺ at m/z = 64, an M+2 peak at m/z = 66 about one-third its height, and a base peak at m/z = 49.
2
Element clue: the M+2 peak at ~⅓ of M⁺ shows one chlorine atom (³⁵Cl : ³⁷Cl ≈ 3 : 1).
3
Mass & fragment: M⁺ = 64 fits chloroethane, C₂H₅Cl (2×12 + 5 + 35 = 64). The base peak at 49 is 64 − 15 = loss of CH₃, leaving CH₂Cl⁺ (12 + 2 + 35 = 49).
4
Answer: chloroethane, CH₃CH₂Cl, identified by mass, the Cl isotope pattern, and the CH₂Cl⁺ fragment.
m/z relative abundance 49 CH₂Cl⁺ 64 M⁺ 66 M+2 64 : 66 ≈ 3 : 1 → one Cl

Chloroethane: the molecular ion at 64 with an M+2 peak at 66 (~⅓ its height) signals one chlorine; the base peak at 49 is the CH₂Cl⁺ fragment after loss of CH₃.

Isotopes: Cl gives M and M+2 ≈ 3 : 1; Br gives M and M+2 ≈ 1 : 1; ¹³C gives a small M+1 (taller with more carbons). Nitrogen rule: odd M⁺ usually means an odd number of N atoms.

Pause, copy the highlighted isotope ratios into your book.

Two peaks of approximately equal height at m/z = 108 and 110 strongly suggest the molecule contains:
5

What Mass Spectrometry Does & Doesn't Tell You

+5 XP

A powerful start, but rarely the whole answer

We just saw how isotopes and fragments add structural clues. That raises a question: is mass spectrometry enough on its own? This card answers it → usually not, it gives mass and clues, but the functional groups and connectivity come from IR and NMR.

Mass spectrometry gives the molecular mass and structural clues from fragments and isotopes, but it rarely gives the full structure alone. It is combined with infrared spectroscopy (functional groups) and NMR (carbon and hydrogen environments) to determine a complete structure, the workflow you build in Lesson 15.

MS gives molecular mass + element/fragment clues, but not functional groups or full connectivity. It is combined with IR (functional groups) and NMR (C and H environments) to determine a structure.

Pause, copy the highlighted limitation note into your book.

Looking ahead: keep the molecular mass from MS in mind, it is the number every other technique has to be consistent with.
A small peak appears one m/z unit above the molecular ion. It is best explained by:
🔬Predict, Then Reveal+8 XP
A spectrum shows M⁺ at m/z = 64, an M+2 peak at m/z = 66 about one-third the height of M⁺, and a base peak at m/z = 49. Predict the element responsible for the m/z = 66 peak and the fragmentation that gives m/z = 49.
Your predictionExpert answerCompare

Complete the Learn phase to unlock Practice.

Activities

ACTIVITY 1, Read the Spectrum

Work through the numbers from peaks alone.

1. A spectrum's highest significant peak is at m/z = 72 and there is a strong peak at m/z = 43. What neutral fragment was lost? (Give its formula.)

2. A compound shows M and M+2 peaks of roughly equal height. Which halogen is present, and why?

3. Why is the base peak not always the molecular ion?

A2

Activity 2, Stages & Reasoning

Connect the instrument to the spectrum.

1. List the five stages of a mass spectrometer in order and state what happens in each.

2. Explain why only positively charged species reach the detector.

3. A molecule has an odd-numbered M⁺. What does the nitrogen rule suggest?

Check Your Understanding

MC

Multiple Choice

1. The m/z value of the molecular ion peak in a mass spectrum is equal to the:

2. A mass spectrum shows two peaks of approximately equal height at m/z = 108 and 110. This strongly suggests the molecule contains:

3. A molecule has M⁺ at m/z = 72 and a strong peak at m/z = 57. The neutral fragment lost is:

4. The base peak in a mass spectrum corresponds to the:

5. A small peak appears one m/z unit above the molecular ion. It is best explained by:

SA

Short Answer

1. A compound shows a molecular ion at m/z = 64 and a peak of roughly one-third its height at m/z = 66, plus a base peak at m/z = 49. Identify the element responsible for the m/z = 66 peak and explain the fragmentation that gives m/z = 49. (4 marks)

2. Explain why the molecular ion is not always the base peak in a mass spectrum. (3 marks)

3. A mass spectrum shows a molecular ion at m/z = 46 and a strong fragment at m/z = 31. Explain how this evidence is consistent with ethanol, and discuss what mass spectrometry can and cannot establish about the structure on its own. (5 marks)

Show All Answers

Activity 1

1. 72 − 43 = 29, so the fragment lost has mass 29 (CHO or C₂H₅).

2. Bromine, ⁷⁹Br : ⁸¹Br ≈ 1 : 1 gives M and M+2 peaks of roughly equal height.

3. The molecular ion often fragments to a more stable cation, which can be more abundant; the base peak is defined as the most abundant ion, so it is frequently a fragment.

Activity 2

1. Vaporisation (sample vaporised) → ionisation (M → M⁺ + e⁻) → acceleration (electric field) → deflection (magnetic field, by m/z) → detection (relative abundance recorded).

2. The instrument accelerates and deflects ions using electric and magnetic fields, which only act on charged particles; neutral fragments are not deflected to the detector.

3. An odd-numbered M⁺ usually indicates an odd number of nitrogen atoms in the molecule (the nitrogen rule).

Multiple Choice

1. B M⁺ equals the molecular mass.

2. B equal-height M and M+2 (≈1:1) indicates one bromine atom.

3. C 72 − 57 = 15, the loss of a CH₃ radical.

4. C the base peak is the most abundant (most stable) cation fragment.

5. B the M+1 peak comes from molecules containing a ¹³C atom.

Short Answer Model Answers

Q1 (4 marks): The peak at m/z = 66 (M+2) at about one-third the height of M⁺ (64) indicates one chlorine atom, because ³⁵Cl : ³⁷Cl ≈ 3 : 1 produces M and M+2 peaks in a ~3 : 1 ratio. The molecular mass 64 fits chloroethane, C₂H₅Cl. The base peak at m/z = 49 is 64 − 15, i.e. loss of a CH₃ radical, leaving the stable chlorine-containing cation CH₂Cl⁺ (12 + 2 + 35 = 49).

Q2 (3 marks): The molecular ion M⁺ often fragments after ionisation. Fragmentation that produces a more stable cation (e.g. a tertiary or secondary carbocation, or a resonance-stabilised ion) is favoured, so a fragment cation can be more abundant than the surviving molecular ion. Since the base peak is defined as the most abundant ion, it is frequently a stable fragment rather than M⁺.

Q3 (5 marks): A molecular ion at m/z = 46 gives a molecular mass of 46, consistent with C₂H₆O (ethanol). The fragment at m/z = 31 is 46 − 15, the loss of a CH₃ radical, leaving CH₂OH⁺ (mass 31), which matches the ethanol structure CH₃CH₂OH. Mass spectrometry can therefore establish the molecular mass and provide structural clues from fragments. However, it cannot directly confirm the functional groups present or the full connectivity, for example it does not by itself distinguish ethanol from its isomer dimethyl ether, so IR and NMR are needed to complete the structure.

Return to Think First

Return to the spectrum with its highest peak at m/z = 46 and a tiny peak at m/z = 47.

  • Which peak is the molecular ion, and what is the molecular mass?
  • What causes the small peak at m/z = 47, and why must you not mistake it for the molecular ion?

Review

What are the five stages of a mass spectrometer?

How do you read the molecular mass from a spectrum, and what is the M+1 trap?

What do isotope ratios for Cl and Br look like?

A peak is 15 mass units below M⁺. What was lost?

Why is mass spectrometry combined with IR and NMR?