Sample is optimally dissolved in water or 10% ACN, 0.1% TFA, and contains minimum salt content (Table).  It is mixed 1:1 with the matrix and spotted  onto MALDI target (spot volume, 0.75 µL).

Commonly used matrices:

alpha-cyano-4-hydroxycinnamic acid (CHCA)

CHCA is the most common matrix used for basic and neutral proteins and peptides.  It is prepared as 5mg/mL in 50% ACN, 50% water, and 0.1% TFA.  Alternatively, instead of water, 25mM ammonium citrate or 6mM ammonium phosphate monobasic can be used to suppress matrix signals.

2,5-dihydroxybenzoic acid (DHB)

DHB is used for acidic and phosphorylated peptides.  It can also be used for organic molecules (carbohydrates, synthetic polymers).  It is prepared as 20mg/mL in 15mM ammonium citrate, 20% ethanol, a 1% phosphoric acid.

sinapinic acid (SA)

SA is generally used for high protein masses (>20kDa).  However, it is particularly appropriate for highly acidic and phosphorylated proteins.  It is prepared as 5mg/mL in 50% ACN, 50% water, and 0.15% TFA.  Alternatively, 25mM ammonium citrate is used instead of water.

2,4,6-trihydroxyacetophenone (THAP)

THAP is used for low mass oligonucleotides (5000Da).  It is prepared as 15mg/mL in 50mM ammonium citrate and 50% ACN.

In addition...

T-2-(3-(4-t-Butyl-phenyl)-2-methyl-2-propenylide) malononitrile (DCTB) is used to analyze fullerene derivatives; dithranol and trans-3-indoleacrylic are used for polymer analysis.