Integration: speeding analysis. Credit: GYROS

Mass spectrometry represents a worldwide market worth US$1 billion a year, with about a third of that dedicated to machines especially suited for proteomics. The system uses three components — an ionization source, an analyser and a detector. Users have at least two choices for each component. Assorted pairings offer different advantages — some combinations are more suited to proteomics, whereas others lend themselves more to small-molecule analysis. And some combinations will integrate with other proteomics equipment such as liquid chromatography. Companies are tending to make their new machines more versatile, more automated and more compatible with other proteomics equipment — but, in general, the more choices offered by one machine, the higher the price tag.

The choices begin where the process starts — ionization sources. Ionization gives the sample an electric charge. The widely used MALDI (matrix-assisted laser-desorption/ionization) uses solid samples, and produces ions of large and small molecules. Electrospray ionization (ESI) is used less often in proteomics. It ionizes liquid samples and is most often used for peptides and small molecules. It can be directly coupled to liquid chromatography systems.

For analysis, time-of-flight (TOF) is most frequently used with MALDI, whereas ESI is usually coupled to quadrupole or ion-trap analysers. Quadrupole machines are considered low-performance instruments compared with MALDI-TOF, but they only cost about a third as much. Ion-trap analysers are also modest performers, but they are robust and easier to look after than the other types, and are even more modestly priced.

Finally, there are two kinds of mass spectrometer — MS and MS/MS. MS is the faster, easier-to-operate option. But, in addition to generating a spectrum of the sample, MS/MS can take some of the ions that have been separated and measured, fragment them further, and then generate spectra of those parts. This allows users to discern which amino acids the peptides contain, and, in some cases, can identify the sequence of these amino acids within the peptide.