1. Sample clean-up (MALDI)
Removal of buffer, salts, urea, guanidine, EDTA, glycerol, DMSO, detergents
Dilution
Washing
Drop Dialysis
Cation Exchange
Zip Tips

2. Typical contaminants in protein/peptide samples
No interference: TFA, formic acid, acetic acid, -mercaptoethanol, DTT, HCl, NH4OH.
Tolerable (<50 mM): HEPES, MOPS, Tris, NH4OAc.
Minimizing buffer concentrations improves performance.
Avoid: Glycerol, sodium azide, DMSO, SDS, phosphate, NaCl, Urea (> 2M), guanidine (>2M)

3. Sample Dilution
The goal is to dilute the contaminants to the point where they no longer interfere with the analysis of the sample.
Requires high enough analyte concentration in the sample to provide acceptable data after dilution.

4. On-Plate Washing Buffer and salt removal Dry sample and matrix
Deposit L cold 0.1% TFA
Leave for sec, then remove
Detergent contamination
use 5% isopropanol - cold
Cell extract contamination
Use 100% isopropanol- cold

5. Drop Dialysis To remove low molecular weight contaminants.
Fill a 250 mL container with ultra pure water.
Float the membrane on the water (shiny side up).
Place L of sample solution on the membrane.
Add 1 L of AcN to sample spot to increase surface area,
Allow to sit for approximately 45 min.
Remove with pipette, add matrix, spot.

6. Cation Exchange For removal of alkali metal ions.
Prepare resin in NH4+ form according to instructions.
Place app. 0.1 mg of beads on a clear piece of parafilm.
Add 5 L of sample and 5 L matrix to beads to make a slurry (the slurry should be app. 50% beads).
Slowly mix up and down with a pipette times.
Allow beads to settle for sec.
Pipette supernatant onto sample plate.
Avoid getting beads onto plate.
Does not work for positively charged species.

7. Solid Phase Extraction - Zip Tip
Zip tip - miniature column chromatography.
Standard C18 zip tips have 0.6 L bed volume.
Micro C18 zip tips have 0.2 L bed volume - better for automation.
C4 zip tips for clean-up of protein samples.
Other types available, e.g. metalchelating for phosphor peptides and cation exchange.

8. Procedure for Zip Tip Use
Condition the tip according to instructions.
Load the sample onto the tip by pipetting L of sample up and down several times and discard the liquid.
Wash with 3 x 10 L 0.1% TFA to remove salts.
Elute the sample using % AcN or matrix.