Mass spectrometry

A mass spectrometer identifies molecules by measuring the mass-to-charge ratio (m/z) of ions derived from a sample, and the instrument's basic logic proceeds in three stages. First, the sample is ionised — commonly by bombarding gas-phase molecules with a beam of electrons energetic enough to knock an electron out of a molecule, producing a positively charged molecular ion. This ionisation step is essential precisely because everything that follows relies on manipulating the resulting ions with electric and magnetic fields, which exert no force on neutral particles. Second, the ions are accelerated and separated according to their m/z ratio — in a magnetic sector instrument, ions moving through a magnetic field are deflected onto curved paths whose radius depends on m/z, so ions of different mass-to-charge ratios physically separate; other instrument designs (time-of-flight, quadrupole) achieve the same separation by different physical means. Third, a detector records the abundance of ions arriving at each m/z value, producing the mass spectrum: a plot of relative abundance against m/z.

The peak corresponding to the intact, unfragmented ionised molecule (the molecular ion peak) gives the compound's molecular mass directly and precisely — often precisely enough to distinguish between molecular formulas that would otherwise be indistinguishable by ordinary mass measurement. But the ionisation process frequently supplies enough excess energy to break some of the molecular ions apart into smaller charged fragments before they are separated and detected, and these fragment ions appear as additional peaks at lower m/z values throughout the spectrum. Rather than being noise to filter out, this fragmentation pattern is itself richly informative: because a molecule tends to break apart at its weaker bonds and in ways that produce more stable fragment ions, the specific pattern of fragment masses acts as a structural fingerprint, often allowing a chemist to work out which functional groups and substructures were present in the original molecule, in addition to knowing its overall mass — which is exactly why mass spectrometry is used throughout organic chemistry, biochemistry, and environmental and forensic analysis both to identify unknown compounds and to confirm the structure of known ones.