The CyDye family of fluorescent dyes is currently the overwhelming choice for 
applications in proteomic analysis, using two-dimensional difference gel 
electrophoresis (2D-DIGE). Protein labeling with CyDyes is hampered by protein 
precipitation and gel smearing when used above minimal labeling. The solubility 
of labeled protein may be improved by introducing water solubilizing groups on 
the dye such as cysteic acids. However, addition of a negatively charged 
functionality will have the undesired effect of shifting the pI in relation to 
the unlabeled protein. These limitations have been addressed through the 
synthesis of highly water-soluble and pI balancing zwitterionic CyDye 
fluorophores (Z-CyDyes). The new dyes feature a cysteic acid motif, a titratable 
amine functionality and a NHS activated ester group. In side by side 2D-DIGE 
comparisons of Z-CyDyes and CyDyes, the new dyes significantly enhanced protein 
spot volume and the number of spots that were detected. Z-CyDyes have the 
potential to enhance the depth of proteome coverage and provide a general 
strategy for improving the performance of protein tagging reagents.