Protein Staining Influences the Quality of Mass Spectra Obtained by Peptide Mass Fingerprinting after Separation on 2-D Gels. A Comparison of Staining with Coomassie Brilliant Blue and Sypro Ruby

Abstract

When separating protein mixtures on 2-D gels for proteomics purposes, fluorescent staining is superior in sensitivity and linear response as compared to Coomassie Brilliant Blue (CBB) and silver staining, respectively. We have compared the quality of mass spectra for proteins obtained from gels stained with CBB and SYPRO Ruby (SR) and found significant differences. These differences can be seen both in inferior signal/noise ratios and number of peptides detected with the fluorescent stain.