The ion sources predominantly used in bioanalysis, especially in peptide and protein analysis, are

• ESI and
• MALDI

ESI
Electrospray ionisation is a soft ionisation method but the analytes have to be soluble in a low-boiling matrix (e.g. acetonitrile, MeOH). A solution of the analyte-matrix-mixture is sprayed under atmospheric pressure through a LC-capillary into a strongly charged field. The high voltage between the tip of the capillary and the obverse electrode is responsible for the fine nebulization and ionisation of the analyte molecules. These molecules are loaded with one or more protons (or Na , K ) coming from the solvent, while the charging depends on the surface of the analyte and therefore represents its secondary or tertiary structure. In this case there are also quasi molecular ions produced, and fragmentation is suppressed. ESI is an applicable method for analysing polar and large biomolecules, polymeric structures and metal complexes which are difficult to vaporise and to ionise. ESI also makes it possible to monitor the folding or unfolding of proteins (Hamdan et al. 2001). Because solvents can be used, ESI can be easily combined with high pressure liquid chromatography (HPLC) or capillary electrophoresis (CE) (Johnson et al. 2001) for separation prior to mass analysis.

MALDI

The matrix-assisted laser desorption/ionisation (MALDI) method is a soft, pulsed laser-ionisation method that can be used for analysis of intact biomolecules, like proteins, after 1-D or 2-D gel electrophoresis separation, and for gathering their sequence or molecular weight information. Methods developed by Tanaka and Hillenkamp allowed the embedding of the analyte into an appropriate organic matrix and a laser pulse (usually nitrogen laser) with a duration of 1-15 ns ablates material from the surface of a matrix-analyte mixture spotted on a metallic target. The laser energy is absorbed by the small organic matrix molecules that are dashed out of the spotted surface, carrying along the analyte molecules. After the subsequent desorption into the vacuum the photoionized radical matrix molecules are able to ionise the analyte molecules through proton transfer. The protonated analyte molecules are accelerated in the electrostatical field towards the mass analyser. Because of its high sensitivity and a minimal fragmentation of the analyte, MALDI is the method of choice for large biomolecules (proteins, oligonucleotides, DNA, RNA) or big synthetic polymers up to 500 kDa (or even 1000 kDa), and polar components. (Marvin et al. 2003; Rehm, 2002)