Differential analysis of cell surface proteins on closed membrane structures by labelling with dyes in the presence of an internal standard

Disclosed are matched fluorescent reagents and a method for reproducibly labelling membrane components, such as those expressed on the cell surface, and subsequent differential analysis of the labelled components to detect differences between cell types and states. Furthermore, the present method utilises an internal standard in order to match protein patterns across gels thereby avoiding gel-to-gel variation. The method according to the invention is particularly useful, for example, for detecting low abundance membrane proteins, for detecting changes in receptors expressed in the cell membrane, for example on ligand binding, or in response to stimuli.