MALDI –TOF SAMPLE PREPARATION GUIDE
1) Washing Stainless Steel MALDI Plate
a. Scrub the sample plate in 2% Decon 90 with a soft nylon brush to remove matrix
deposits.
b. Rinse the plate in distilled water.
c. Sonicate for 10 minutes in 1:1 dichloromethane: methanol when analysing synthetic
polymers.
d. Sonicate for a further 10 minutes in methanol.
e. Dry under a dry nitrogen stream.
You will need to purchase your own MALDI plate from Waters (96) Product Number: M880373BD1-S
2) Matrix Information
Matrix
Sinapinic acid-SIN
(MW=224.07 Da)
α-cyano-4-hydroxycinnamic acid-CHCA
(MW=189.04 Da)
trans-2-[3-(4-tert-Butylphenyl)-2methyl-2-propenylidene]malononitrileDCTB
3-hydroxypicolinic acid- HPA
(MW=139.03 Da)
“Super-DHB”- S-DHB
2′,4′,6′-Trihydroxyacetophenone
monohydrate-THAP
(MW=168.04)
2.5-dihydroxybenzoic acid-DHB
(MW=154.03 Da)
2-(4-Hydroxyphenylazo)benzoic acidHABA
(MW=242.07 Da)
Applications
Proteins/ Large peptides
Peptides
Polymers
Oligonucleotides
Large Oligonucleotides
Small Oligonucleotides
Sugars/peptides/polymers
Proteins/ Polar and nonpolar synthetic
polymers/Glycolipids
3) Matrix preparation:
A. Sinapinic acid-SIN
Use a concentration of 10mg/ml in 40:60 acetonitrile: 0.1% TFA (aq.). Sonicate the
solution for 10 mins. Mix matrix to sample at a ratio of 1:1.
To improve signal, mix sinapinic acid at a ratio of 3:1 matrix to sample.
B. α-cyano-4-hydroxycinnamic acid-CHCA
Use a concentration of 10mg/ml in 50:50 acetonitrile: 0.1% TFA (aq.). Sonicate the
solution for 10 mins. Mix matrix to sample at a ratio of 1:1.
.
C. trans-2-[3-(4-tert-Butylphenyl)-2-methyl-2-propenylidene]malononitrile- DCTB
Use a concentration of 40mg/ml in Tetrahydofuran- THF and prepare a 5mg/ml of
Potassium Trifluoroacetate- KTFA solution in THF. Mix 10µl of sample +10 µl of
DCTB and add 2.5 µl of KTFA.
D. 3-hydroxypicolinic acid- HPA
Use a concentration of 50mg/ml in 10mg/ml of ammonium citrate. Mix matrix to
sample at a ratio of 1:1.
E. 2.5-dihydroxybenzoic acid-DHB
Use a concentration of 10mg/ml in 70:30 water: acetonitrile. Mix matrix to sample at
a ratio of 1:1.
F. “Super-DHB”- S-DHB
Add 1 mg of S-DHB to 9 mg of DHB. Dissolve the mixture in 9:1 0.1%TFA (aq.):
acetonitrile. Mix matrix to sample at a ratio of 1:1
G. 2′,4′,6′-Trihydroxyacetophenone monohydrate-THAP
Use a concentration of 25mg/ml in 50:50 water: acetonitrile. Use this matrix together
with an ammonium salt solution. Mix matrix to sample at a ratio of 1:1
H. 2-(4-Hydroxyphenylazo)benzoic acid-HABA
Use a concentration of 3.5 mg/ml in methanol. Mix matrix to sample at a ratio of 1:1.
4) Crystallization:
Spot 0.5–1 μl of matrix onto the sample plate and add 0.5–1 μl of sample, mix both
with the micropipette and allow to air dry or prepare a mixture of 5-10µl of matrix +
5-10µl of sample, vortex and spot 1-2µl onto the sample plate and air dry.
MALDI Plate