The standard protocols performed in Proteomics Core are listed below:
2D Gel electrophoresis
To help you in your sample analysis, we have included web links to the companies and Swiss Institute of Bioinformatics for the sample preparation and 2D Gel Electrophoresis guidelines.

From: ExpASy server (, Bio-Rad 2D Gel Electrophoresis manual
(, Amersham Biosciences ( (PDF attached)

2D Gel Electrophoresis Sample Submission Form

Sample solution is suggested in buffer: *<10mM salt and buffer (ideally no salt or buffer) *Avoid ionic components (such as SDS). * Can contain 4% CHAPS and 8M urea (the IPG sample loading buffer) * Concentration: 5-10 mg/ml. *Amount: total volume of 185ul and 20-200ug for 11 cm strips if you wish to submit raw samples for extraction, please contact Biomedical Proteomics Facility staff for further information.

For assuring the successful analysis, we recommend that the amount of protein sample for MS analysis is more than 50 mg per sample (1D gel band or 2D gel spot). ~10-50 ng per gel sample may be analyzed by MS and yield an acceptable result. A rule of thumb is that it is likely identified if the band or spot can be observed in Coomassie.

Often, the faint spots visualized with Sypro Ruby or CyDyes may not yield good MS results due to the much lower detection limit of fluorescence imaging methods. Sample origin (taxonomy) should be specified in the sample submission form to facilitate database searching of the mass spectrometry data.