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A mass spectrometer is, in a sense, an extremely precise weighing machine for individual atoms and molecules. It can tell apart atoms that differ in mass by a single neutron, identify a drug from a few nanograms in a blood sample, and reveal the structure of an unknown molecule from the pieces it breaks into. It’s how the relative atomic masses on the periodic table were measured, and it’s one of the most powerful tools in modern chemistry.
The big idea
A mass spectrometer:
- turns atoms or molecules into ions (charged particles),
- separates them according to their mass-to-charge ratio (m/z), and
- detects how many ions of each m/z value there are.
For most ions in school and college work, the charge is +1, so m/z is simply the mass of the ion. The output is a mass spectrum: a graph of relative abundance (or intensity) against m/z.
Inside a time-of-flight (TOF) mass spectrometer
Many courses describe the time-of-flight design. It has four stages, all inside a vacuum (so ions don’t collide with air molecules):
1. Ionisation
The sample is turned into positive ions. Two common methods:
- Electron impact (EI): the sample is vaporised and bombarded with high-energy electrons from an electron gun. These knock an electron out of each atom or molecule: X(g) + e⁻ → X⁺(g) + 2e⁻ Molecules often break apart (fragment) during this process.
- Electrospray ionisation (ESI): the sample is dissolved in a volatile solvent and sprayed through a fine, high-voltage needle. Molecules pick up a proton: X(g) + H⁺ → XH⁺(g) This is a “soft” method that causes little fragmentation, so it’s ideal for large molecules such as proteins. Note that the detected ion has a mass one unit higher than the molecule (M + 1).
2. Acceleration
An electric field accelerates all the positive ions so they have the same kinetic energy.
3. Ion drift (flight)
The ions travel through a field-free flight tube. Since they all have the same kinetic energy, KE = ½mv², lighter ions travel faster and heavier ions travel slower.
4. Detection
Ions hit a detector at the end of the tube. Lighter ions arrive first. Each ion picks up an electron from the detector, producing a current. The size of the current tells you how many ions arrived; the arrival time tells you their mass.
The time of flight relates to mass as t = d × √(m ÷ 2KE), where d is the length of the tube. Other designs (magnetic sector, quadrupole, Orbitrap) separate ions differently, but the principle of sorting by m/z is the same.
Reading the mass spectrum of an element
For an element, each peak corresponds to one isotope. The height (or abundance) of each peak shows how common that isotope is.
Example: chlorine
| m/z | Relative abundance |
|---|---|
| 35 | 75.8% |
| 37 | 24.2% |
Calculating relative atomic mass
The relative atomic mass (Ar) is the weighted mean of the isotope masses:
Ar = Σ(isotope mass × abundance) ÷ Σ(abundance)
Chlorine: Ar = (35 × 75.8 + 37 × 24.2) ÷ 100 = (2653 + 895.4) ÷ 100 = 35.48 (35.5 to 3 s.f.)
Example with relative intensities (not percentages): magnesium gives peaks at m/z 24, 25 and 26 with relative intensities 78.99, 10.00 and 11.01.
Ar = (24 × 78.99 + 25 × 10.00 + 26 × 11.01) ÷ (78.99 + 10.00 + 11.01) = (1895.76 + 250.0 + 286.26) ÷ 100.00 = 24.32
This is how the atomic masses shown on the periodic table were determined. More practice is in mass spectra for elements and isotopes.
Mass spectra of molecules
For a compound, the spectrum usually shows:
The molecular ion peak (M⁺)
The peak for the whole molecule minus one electron. It’s usually the peak with the highest m/z (ignoring small isotope peaks), and it gives the relative molecular mass (Mr).
For example, ethanol (C₂H₅OH, Mr = 46) has a molecular ion peak at m/z 46.
The M+1 peak
A small peak one unit above M⁺, caused by molecules containing a carbon-13 atom. About 1.1% of carbon atoms are ¹³C, so the M+1 peak’s height is roughly 1.1% × (number of carbon atoms) of the M⁺ peak. That lets you estimate how many carbons a molecule has.
Halogen patterns
- Chlorine (³⁵Cl : ³⁷Cl ≈ 3 : 1): a compound with one Cl atom shows M and M+2 peaks in a 3 : 1 ratio.
- Bromine (⁷⁹Br : ⁸¹Br ≈ 1 : 1): a compound with one Br atom shows M and M+2 peaks of nearly equal height.
These patterns make chlorine and bromine compounds easy to spot.
Fragment peaks
With electron impact ionisation, many molecular ions break into smaller pieces. Only charged fragments are detected. The pattern of fragments is characteristic of the molecule and helps identify it.
| Fragment lost / formed | m/z | Suggests |
|---|---|---|
| CH₃⁺ | 15 | methyl group |
| C₂H₅⁺ | 29 | ethyl group (or CHO⁺) |
| CH₃CO⁺ | 43 | methyl ketone or ethanoyl group (also C₃H₇⁺) |
| C₆H₅⁺ | 77 | benzene ring |
| M − 15 | loss of CH₃ | |
| M − 18 | loss of H₂O (common for alcohols) |
The tallest peak in the spectrum is called the base peak; it’s assigned an abundance of 100%, and it corresponds to the most stable, most abundant fragment. It isn’t always the molecular ion.
Example: propanone (CH₃COCH₃, Mr = 58) shows M⁺ at m/z 58, and a large base peak at m/z 43 from the CH₃CO⁺ fragment formed by losing a CH₃ group.
High-resolution mass spectrometry
High-resolution instruments measure m/z to four or more decimal places. Because isotopes don’t have exactly whole-number masses (¹H = 1.0078, ¹²C = 12.0000, ¹⁶O = 15.9949, ¹⁴N = 14.0031), molecules with the same nominal mass can be told apart:
| Formula | Nominal mass | Accurate mass |
|---|---|---|
| CO | 28 | 27.9949 |
| N₂ | 28 | 28.0061 |
| C₂H₄ | 28 | 28.0313 |
An accurate mass measurement can therefore pin down a molecule’s molecular formula.
Worked example: identifying a compound
A compound gives a molecular ion at m/z 74 and a strong fragment peak at m/z 45. Its M+1 peak is about 3.3% of the M⁺ peak. Suggest a formula.
- M+1 ratio ≈ 3.3% ÷ 1.1% ≈ 3 carbon atoms.
- Mr = 74 with 3 carbons: C₃H₆O₂ fits (3 × 12 + 6 × 1 + 2 × 16 = 74).
- A fragment at 45 could be COOH⁺, suggesting a carboxylic acid: propanoic acid, CH₃CH₂COOH.
Infrared spectroscopy (a broad O–H and a C=O peak) would confirm the carboxylic acid group.
Uses of mass spectrometry
- Measuring relative atomic masses and isotope abundances.
- Identifying unknown compounds, often combined with gas or liquid chromatography (GC–MS, LC–MS). See gas chromatography.
- Drug testing in sport and forensics.
- Radiocarbon dating by accelerator mass spectrometry, which counts carbon-14 atoms directly. See carbon-14 dating.
- Space exploration: mass spectrometers on Mars rovers and planetary probes analyse rocks and atmospheres.
- Medicine: newborn screening for metabolic disorders, and identifying bacteria from their protein fingerprints.
- Proteomics: identifying and sequencing proteins.
Key takeaways
- A mass spectrometer ionises particles, accelerates them, separates them by m/z and detects them.
- In time-of-flight instruments, lighter ions travel faster and arrive first.
- For elements, peaks show isotopes; Ar is the weighted mean of isotope masses.
- For molecules, the molecular ion gives Mr; fragments and isotope patterns help identify the structure.
- High-resolution MS gives accurate masses that determine molecular formulas.
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