Matrix Recipes

There is some technique to getting good MALDI-TOF results for different classes of compounds.  Some recipes are presented here which work when using different MALDI matrices.  Remember, always use the highest purity matrices and solvents, and recrytalize the matrix if necessary.  Matrix should be freshly prepared each time and can be mixed with sample in a 1:1 ratio prior to spotting. 

1.  Sinapinic Acid (used for proteins)

  • Use 0.5 ml tube and cover bottom with matrix
  • Add 300 uL acetonitrile/water 50:50 with 0.1% TFA
  • Shake/vortex well. This will produce a saturated solution with some matrix on the bottom.

2.  Alpha-cyano-4-hydroxycinnamic acid (used for peptides <10 kDa)

  • A. A saturated solution in acetnitrile/water 50:50, 0.1% TFA
  • B. Alternatively, 4 mg/ml in 700 μL of 50:50 water acetonitrile/water.  300  μL of acetone.  The acetone is added to increase solubility of the matrix in the solvent!

3. DHB (2,5 Dihdroxybenzoic Acid)

15 mg into 1 ml methanol

4. THAP Mix (typically used with oligonucleotide samples)

Sodium removal is critical when analyzing oligo samples.  The presence of trace amounts of sodium can form abundant adducts lowering the signal to below detection.  Dibasic citrate is sometimes used to reduce this effect.

  • 18 mg of Trihydroxyacetophenone
  • 5 mg ammonium citrate, dibasic (to chelate away sodium)
  • Dilute into 1 ml acetonitrile:water 50:50

5.  HPA or 3-Hydroxypicolinic Acid (HPA-typically used with oligonucleotide samples)

  • 0.7M (97mg/ml) 3-hydroxypicolinic acid
  • 0.07M (16 mg/ml) ammonium citrate (sodium removal as with THAP for sensitive oligo samples)
  • Dilute with 1 ml acetonitrile:water 50:50 v/v