Hi Constanza,

Throughout the electrophoresis steps, please use powder free gloves to prevent contamination from skin keratins. It is also important to dedicate apparatus for electrophoresis and not to use any surfaces used for Western blots. Otherwise, you will encounter eg., casein and BSA contamination arising from blocking of membranes during Western blots.

The best way to clean any glass apparatus to remove background proteins is the following procedure: this is the same procedure our proteomics laboratory at MSKCC used, for high sensitivity sequencing of peptides:

1: RInse glassware with 80% acetic acid (v/v)

2: Follow 1 above with MQ filtered water

3. Follow 2 with 100% methanol

4: Follow 3 with MQ filtered water.

This protocol of stringent washes can completely remove any protein/peptide contamination from your elelctrophoresis apparatus. Please use a fume hood for this cleaning experiment. Also, make sure your electrophoresis containers are glass eg;, pyrex glass containers that can be used for stainng and washing of the gels.

The plastic containers used for electrophoresis can be rinsed with dilute methanol and water. You can omit the acetic acid for these plastic containers.

Good luck!

Hediye.