Mass spectrometry

CIE A-Level Chemistry· Unit 16: Introduction to analytical chemistry· 15 min read

1. 1. Key Stages of Mass Spectrometer Operation★★☆☆☆⏱ 4 min

Mass spectrometry separates positive ions based on their mass-to-charge ratio ( $m / z$ ) to produce a spectrum that gives information about the mass and relative abundance of particles.

📘 Definition

Mass-to-charge ratio (m/z)

The ratio of the mass of an ion (in atomic mass units, u) to its charge (in number of elementary charges, e). Most detected ions are +1, so m/z equals the mass of the ion.

Example:

A singly charged ion of mass 44 u has m/z = 44

Ionisation: The sample is bombarded with high-energy electrons to form positive ions.
Acceleration: Positive ions are accelerated by an electric field to constant kinetic energy.
Deflection: Ions are deflected by a magnetic field; lighter/ higher charge ions are deflected more.
Detection: Ions reach a detector, and their abundance and m/z are recorded.

2. 2. Calculating Relative Atomic Mass from Isotopic Spectra★★☆☆☆⏱ 6 min

For an element with multiple isotopes, mass spectrometry measures the mass and relative abundance of each isotope, which we use to calculate the weighted average relative atomic mass ( $A_{r}$ ).

📐 Worked Example

A sample of neon has three isotopes with the following mass and percentage abundance: $^{20}$ Ne (19.99, 90.5%), $^{21}$ Ne (20.99, 0.3%), $^{22}$ Ne (21.99, 9.2%). Calculate the relative atomic mass of neon.

1
Relative atomic mass is calculated as the weighted average of isotopic masses, using the formula:
2
$A_r = \frac{(m_1 \times a_1) + (m_2 \times a_2) + ... + (m_n \times a_n)}{100}$
3
Substitute the values from the question into the formula:
4
$A_r = \frac{(19.99 \times 90.5) + (20.99 \times 0.3) + (21.99 \times 9.2)}{100}$
5
Calculate the numerator, then divide by 100 to get the final value:
6
$A_r = \frac{2017.7}{100} = 20.18 \text{ (4 s.f.)}$

✓ Quick check

Check your understanding

Chlorine has two isotopes: $^{35}$ Cl (75% abundance) and $^{37}$ Cl (25% abundance). What is the $A_{r}$ of chlorine?
- 35.0
- 35.5
- 36.0
- 36.5
Reveal answer
35.5 —
Correct: $(35 \times 75 + 37 \times 25) /100 = 35.5$

3. 3. Interpreting Organic Mass Spectra★★★☆☆⏱ 6 min

For organic compounds, mass spectrometry provides information about the molecular mass and structure of the compound, via the molecular ion and fragment peaks.

📘 Definition

Molecular ion ($M^+$)

M^+ peak at m/z = M_r

The whole organic molecule ionised after losing one electron. The m/z of this peak equals the relative molecular mass ( $M_{r}$ ) of the compound.

📘 Definition

Base peak

The most abundant (tallest) peak in the mass spectrum, always assigned an abundance of 100%.

Example:

Often the most stable fragment ion, e.g. the acylium ion at m/z 43 in aliphatic ketones

📐 Worked Example

A straight chain alkane has a molecular ion peak at m/z = 72. What is its molecular formula?

1
For +1 ions, the m/z of the molecular ion equals the relative molecular mass, so $M_{r} = 72$ . The general formula for an alkane is $C_{n} H_{2 n + 2}$ .
2
Substitute atomic masses (C = 12, H = 1) to solve for n:
3
$12n + (2n + 2) = 72 \\ 14n = 70 \\ n = 5$
4
The molecular formula is confirmed to be $C_{5} H_{12}$ , as $12 (5) + 12 (1) = 72$ .

4. 4. Identifying Common Fragment Ions★★★☆☆⏱ 5 min

When the molecular ion breaks apart during ionisation, it forms stable fragment ions that give clues about the structure of the original molecule. Common fragments correspond to common functional groups or alkyl groups.

Fragment	m/z value	Common origin
CH $_{3}^{+}$	15	Alkyl chains
C $_{2}$ H $_{5}^{+}$	29	Ethyl groups/alkanes
CO^+$	28	Aldehydes/ketones
CH $_{3}$ CO^+$	43	Ethanoyl groups/ketones
C $_{6}$ H $_{5}^{+}$	77	Aromatic benzene rings
COOH^+$	45	Carboxylic acids

5. Common Pitfalls

Wrong move:

Writing the order of stages as Ionisation → Deflection → Acceleration → Detection

Why:

Ions must be accelerated to uniform kinetic energy before deflection can separate them by mass

Correct move:

Memorise the order: Ionisation → Acceleration → Deflection → Detection

Wrong move:

Calculating $A_{r}$ as the simple average of isotopic masses, ignoring abundance

Why:

This does not account for different proportions of each isotope, leading to incorrect results

Correct move:

Always calculate the weighted average: multiply each mass by its percentage abundance, sum, then divide by 100

Wrong move:

Assuming the tallest (base) peak is the molecular ion peak

Why:

The base peak is the most abundant fragment, not the whole molecular ion, so this gives the wrong $M_{r}$

Correct move:

The molecular ion is the highest significant m/z peak (excluding the small M+1 peak)

Wrong move:

Dividing m/z by 2 for all ions to get mass

Why:

Almost all ions detected in standard mass spectrometry are singly charged (+1)

Correct move:

Only adjust for charge if the question explicitly states the ion has a +2 or higher charge

6. Quick Reference Cheatsheet

Concept	Key Fact
Stage order	Ionisation → Acceleration → Deflection → Detection
m/z for +1 ions	Equals the mass of the ion
Relative atomic mass	$A_{r} = \sum (m_{i} \times a_{i}) /100$
Molecular ion peak	Gives the relative molecular mass $M_{r}$
Base peak	Most abundant peak = 100% abundance
CH $_{3}^{+}$ fragment	m/z 15, M-15 = CH $_{3}$ loss
C $_{6}$ H $_{5}^{+}$ fragment	m/z 77, indicates benzene ring

When this came up on past exams

AI-estimated based on syllabus patterns — cross-check with official past papers for accuracy. Use only as revision-focus signals.

2022 · 12
Calculate relative atomic mass from spectrum
2023 · 22
Identify fragments from organic mass spec
2021 · 13
Describe mass spectrometer stages

Going deeper

syllabusCIE 9701 2025-2026 SyllabusUnit 16 content overview

What's Next

Mass spectrometry is a core analytical technique that forms the foundation for advanced structural problem-solving in organic chemistry, a common extended question in CIE 9701 papers. You will combine mass spectrometry data with data from other spectroscopic techniques to identify unknown organic compounds, a key skill for Paper 2 and Paper 4. Understanding mass spectrometry also supports the study of isotopic labelling used to investigate reaction mechanisms. Mastering the skills here will make more advanced analytical topics much easier to tackle.