the present invention relates to methods for identification and quantification of proteins expressed within a cell . the methods of the invention involve the separation of proteins based on their physical properties such as , for example , net charge , molecular weight , or immunoreactivity , followed by detection of said proteins using a number of different techniques including ramification - extension amplification method ; hybridization signal amplification method ; and detection with nanodots . the methods of the invention will have a variety of different uses including , but not limited to , uses for screening , for diagnosis and prognosis of disease . the methods of the invention are especially useful for identification of proteins that are not easily identified due to the small size of the protein , low concentration of the protein , or failure to separate proteins due to similar physical properties .