How a Mass Spectrometer Works

Introduction

Infrared spectroscopy tells you which functional groups are present, but it cannot weigh a molecule. A mass spectrometer can. It converts a tiny sample — often less than a microgram — into charged particles, sorts them according to their mass and charge, and counts how many of each arrive. The output, a mass spectrum, gives the relative molecular mass of a compound and clues to its structure. Before interpreting spectra you need a clear picture of what happens inside the machine, because every feature of a spectrum traces back to one of its stages.

Core explanation

All mass spectrometers share four essential stages, and the whole instrument is kept under a high vacuum . The vacuum matters: if air molecules were present, the ions would collide with them, be deflected at random or lose their charge, and never reach the detector in an orderly way.

1. Ionisation. Neutral molecules cannot be steered by electric or magnetic fields, so they must first be given a charge. Two methods are common.

- Electron impact (EI). The sample is vaporised and bombarded with a beam of high-energy electrons (typically 70 eV) from a hot filament. A collision knocks an electron out of the molecule: M(g) + e⁻ → M⁺•(g) + 2e⁻ The product M⁺• is a radical cation (positive and with an unpaired electron) called the molecular ion. EI transfers so much energy that many molecular ions break into fragments, which is useful for structure determination. - Electrospray ionisation (ESI). The sample is dissolved in a volatile solvent and sprayed through a fine needle held at a high voltage. Droplets shrink as solvent evaporates, and molecules emerge carrying an extra proton: M + H⁺ → [M+H]⁺ ESI is a "soft" method: little fragmentation occurs, so it suits large, fragile molecules such as proteins. Note that the ion detected has a mass one unit greater than the molecule.

2. Acceleration. Positive ions are attracted towards a negatively charged plate and pass through it. An electric field gives every ion of the same charge the same kinetic energy .

3. Separation. This is where instruments differ.

- In a time-of-flight (TOF) instrument, ions enter a field-free drift region of known length. Since kinetic energy = ½mv² is the same for all singly charged ions, lighter ions travel faster and arrive first; heavier ions lag behind. - In a magnetic sector instrument, a magnetic field bends the ion beam. Light ions are deflected more than heavy ones; by varying the field strength, ions of each mass-to-charge ratio are focused on the detector in turn.

4. Detection. Ions striking the detector gain electrons (or release a cascade of electrons in an electron multiplier), producing a small current. The size of the current is proportional to the number of ions, so the instrument records their relative abundance . A computer then plots abundance against mass-to-charge ratio.

Formulae

Kinetic energy of an ion: KE = ½mv², so v = √(2KE ÷ m). Time of flight across a drift region of length d: t = d ÷ v = d√(m ÷ 2KE). Because KE and d are fixed, t ∝ √m for ions of equal charge. Mass m is in kg (1 u = 1.661 × 10⁻²⁷ kg).

Step-by-step reasoning

To follow one molecule of propanone through an EI time-of-flight instrument:

1. The liquid is vaporised into the ionisation chamber. 2. An electron collision removes one electron, forming CH₃COCH₃⁺•. 3. The electric field accelerates the ion; it gains the same kinetic energy as every other singly charged ion. 4. In the drift region it moves at a speed fixed by its mass, arriving after lighter fragment ions. 5. At the detector it produces a pulse of current recorded against its flight time, which the software converts to m/z = 58.

Visual explanation

Picture a straight tube. At the left end sits the ionisation source, then a pair of charged grids, then a long empty drift tube, then the detector at the right. Ions leave the grids together like runners at a starting gun; the smallest reach the detector first and the heaviest last, giving a series of spikes in time.

Real-world analogy

Imagine rolling a table-tennis ball and a cricket ball with the same push of energy. The light table-tennis ball zooms across the floor; the heavy cricket ball moves slowly. Time how long each takes to cross the room and you can deduce which is heavier — exactly the principle of time of flight.

Real-world example

Airport security scanners and anti-doping laboratories rely on mass spectrometry. In sports testing, urine extracts are separated by chromatography and fed into a mass spectrometer; a banned steroid is identified by the precise masses of its ions, even at concentrations of nanograms per millilitre.

Why?

Why must the ions be charged before they can be analysed? Electric and magnetic fields exert forces only on charged particles. A neutral molecule would drift straight through the instrument unaffected, so there would be no way to accelerate, separate or detect it. Ionisation is what makes the molecule "visible" to the machine.

Common misconception

"A mass spectrometer measures mass directly." It does not: it measures how ions behave in fields, which depends on the ratio of mass to charge. An ion carrying two charges behaves like one of half the mass, so the instrument really records mass-to-charge ratio.

Worked example

Question: In a TOF spectrometer, CO₂⁺ (m/z 44) and N₂⁺ (m/z 28) are given the same kinetic energy. N₂⁺ takes 20.0 μs to reach the detector. Estimate the flight time of CO₂⁺.

Reasoning: t ∝ √m, so t(CO₂⁺) = 20.0 × √(44 ÷ 28) = 20.0 × 1.254 = 25.1 μs.

Answer: About 25.1 μs; the heavier ion arrives later.

Quick check

1. Why is a high vacuum maintained inside every mass spectrometer, from the ion source to the detector? Answer: So that ions do not collide with air molecules, which would deflect them or neutralise them before they reach the detector.

Exam focus

Be ready to name and describe the four stages in order and to write an ionisation equation with state symbols, for example M(g) + e⁻ → M⁺(g) + 2e⁻. For ESI, remember the ion is [M+H]⁺. TOF calculations rearrange KE = ½mv²; always convert the ion mass into kilograms and time units consistently.

Advanced insight

Modern instruments often combine techniques. In tandem mass spectrometry (MS/MS), ions of one chosen m/z are isolated, deliberately broken by collision with an inert gas, and the fragments analysed in a second stage. Orbitrap analysers trap ions in an electric field and measure the frequency of their oscillation, which depends on m/z and allows resolution of masses differing by a few parts per million.

Summary

A mass spectrometer ionises a sample (by electron impact to give M⁺•, or by electrospray to give [M+H]⁺), accelerates the ions so they share the same kinetic energy, separates them by flight time or magnetic deflection, and detects them as a current proportional to abundance. Everything happens under high vacuum, and the instrument really sorts ions by mass-to-charge ratio.

Practice questions

1. Write an equation, with state symbols, for the electron impact ionisation of methane. Answer: CH₄(g) + e⁻ → CH₄⁺•(g) + 2e⁻ 2. A molecule of relative mass 180 is analysed by electrospray ionisation. At what m/z will its main ion appear, and why? Answer: At m/z 181, because the molecule gains a proton to form [M+H]⁺. 3. Explain why lighter ions reach the detector first in a time-of-flight instrument. Answer: All ions have the same kinetic energy, ½mv², so ions of smaller mass must have greater speed and cross the drift region in less time. 4. Why is electrospray preferred over electron impact for analysing a protein? Answer: Electrospray is a soft technique that ionises the large molecule without breaking it into many fragments, so the molecular ion can still be observed.