When preparing samples for mass spectrometric analysis, it is best to limit sample manipulations. When dealing with solution samples, never bring the sample to complete dryness. Salts and detergents will interfere with MS analysis of solution samples. Based on extensive studies, we have found that SDS-PAGE or 2D IEF-SDS-PAGE is the best method for recovery of low quantities of protein.
Suggested method for staining gels with Coomassie Blue G-250
It is important to run and process the gel in as clean an environment as possible. Use thoroughly washed or disposable labware, wear gloves, and make sure reagents are fresh and uncontaminated.
You should clean a glass or plastic tray with detergent and rinse it thoroughly. You should wear clean, disposable gloves and never touch the gel bands directly. Never reuse stains and thoroughly acid wash staining trays if you reuse them.
Protein gels can also be stained with Gel Code Blue (Pierce). We have obtained nanogram-level detection of proteins with the Colloidal Blue Staining Kit (INVITROGEN). Please follow instructions from the manufacturer.