Mass spectrometry

Mass spectrometry ionises a sample and measures the mass-to-charge ratio of the resulting ions. For peptides the measured mass is compared against the mass calculated from the intended sequence, including any specified terminal modifications.

Resolution and accuracy

Two distinct properties determine what a measurement can support. Resolution describes the ability to distinguish ions of similar mass; accuracy describes how close a measured mass is to the true value. High-resolution instruments can resolve the isotopic pattern of a peptide, which itself carries compositional information, whereas lower-resolution measurement returns an average mass with correspondingly weaker discrimination.

Fragmentation and sequence confirmation

Tandem mass spectrometry selects an ion, fragments it, and measures the products. Because fragmentation occurs preferentially at peptide bonds, the resulting series can be read to confirm residue order. This distinguishes sequences that share a total mass and is the step that turns a consistent mass into a supported identity.

Mass spectrometry is also poorly suited to quantifying relative amounts without careful calibration, because ionisation efficiency differs between species. A small peak in a mass spectrum does not reliably indicate a small quantity.