AP/MALDI Sample Preparation Protocols

Preparation of MALDI matrix:

We recommend dissolving 1-1.25 mg/mL of α-Cyano-4-hydroxycinnamic acid (Fluka, Buch, Switzerland, P/N 28480) into a solution of 70% ACN (Sigma, St. Louis, MO, USA) and 0.1% TFA (Sigma, St. Louis, MO, USA) in water (Molecular Biology Grade, Biowittaker, Walkersville, MD, USA). The matrix solution should be stored in the dark at room temperature and used for no more than 1 week, then discarded.  The ready-to-use CHCA matrix solution is also available from MassTech, Inc. (Part No. MAT90).

Target plate cleanup:

For MassTech gold-plated targets: Targets should be handled with a care to prevent scratching the gold coat surface. Prior to applying the sample for AP-MALDI analysis we recommend the following procedure for cleaning the target plates:

1. Wash the target plate with Acetone.
2. Wash the target plate with Methanol and de-ionized water (v/v 1:1).
3. Wash target plate with de-ionized water.
4. Let the plate to completely dry before applying samples.

NOTE: Target plate sonication should be done only in case residues are observed on the surface. A soft cleaning procedure below is highly recommended: (a) sonicate plate 10-15 min in 50% methanol with diluted detergent (Alconox, Inc.); (b) rinse plate thoroughly with running water; (c) sonicate for 5 min in de-ionized water;  (d) wash with de-ionized water again before air dry.

Preparing samples:

Sample Preparation Method 1:

1. Prepare your protein/peptide solution diluting it with the matrix solution as a solvent to achieve the desired analyte concentration.
2. Place 1.0-2.0 µl of the above analyte/matrix solution onto the target plate.
3. Allow the sample to air dry naturally.

Sample Preparation Method 2:

1. Prepare your protein/peptide solution diluting it by 0.1% TFA solution to get the desired analyte concentration.
2. Apply 1 µl of the analyte solution onto the target plate.
3. Add 1 µl of the matrix solution on the top of the analyte sample.
4. Allow the sample to air dry naturally.