α-Cyano-4-hydroxycinnamic acid (α-Cyano; HCCA; CCA)
Commonly used for peptides in the lower mass range.
Not soluble in water and well soluble in organic solvents.
It is considered a "hard" matrix, which means the analyte molecules get a lot of internal energy during desorption and ionization. This leads to a considerable amount of ion fragmentation (post source decay - PSD). If peptides of small molecular weight are measured and the laser power is chosen only slightly above the threshold, this is not a problem. If the analyte molecules become bigger, however, the probability of the fragmentation increases until almost all of the analyte ions undergo fragmentation. Therefore α-Cyano is the matrix of choice for PSD-analysis.
The main advantage of α-Cyano in the measurement of peptides is the ability of this matrix to form small homogenous crystals. Since geometric inhomogeneity relates directly to decreased resolution in the MALDI-analysis, α-Cyano preparations usually yield good resolution.
Sinapinic Acid (SA)
Sinapinic Acid is most commonly used in the analysis of high mass proteins.
Not soluble in water but well soluble in organic solvents.
Compared to α-Cyano it is a "softer" matrix. The analyte Ions get less internal energy and the amount of fragmentation is smaller, making this matrix more suitable for measurement of proteins. Sinapinic Acid also can form small crystals. However, Sinapinic Acid tends to form adducts with the analyte ions. These adducts can be resolved in the mass spectrum for proteins up to 40 kD.
2,5-Dihydroxybenzoic acid (DHB)
This is the matrix of choice for the preparation of glycoproteins and glycans. It is also often used for peptides.
Unlike α-Cyano and Sinapinic Acid it is soluble in water as well as organic solvents.
The main disadvantage of DHB is the fact that it forms big crystal needles. This means that the geometry of the sample changes from spot to spot. If spectra are summed up from different spots on the sample, the resolution is considerably lower than spectra obtained from an α-Cyano.
On a steel target, DHB preparations will form a crystalline ring. Good peptide spectra are usually only obtainable at the rim.
The main advantage of DHB for MALDI of peptides is the fact that this matrix is more tolerant towards contaminations.