My wife can attest to the Economist's just released technology report detailing the difficulties of developing a protein chip.  Three years ago she left a UCSF/Stanford's Doctoral program in Neuroscience with a post-doc friend to start a protein chip company, Aspira Biosystems.

Protein chips promise to accurately and inexpensively capture and identify proteins, just as gene chips now enable reliable and efficient genetic analysis.  The development of effective protein chips is a critical link in the development of personalized medicine.

Designing a protein chip is not easy, requiring expertise from a wide variety of disciplines including, protein chemistry, materials science and surface chemistry.  As the article poignantly declares, "a protein chip is to a gene chip what a supercomputer is to a calculator."

DNA is simpler to analyze than proteins for several reasons:

• DNA has four building blocks, proteins have 20 amino acid building blocks
  
• Genes code for the one purpose of producing proteins, proteins serve multiple purposes as enzymes, receptors, signaling agents
  
• The genome is a relatively well-defined collection of about 40,000 genes, but the proteome is a loose collection of millions of proteins at different stages of change

Aspira's competitive advantage stems from their abilty to generate capture arrays with predictable specificity.  Thanks to incredible dedication and continued private and public funding, Aspira is poised to leap to the forefront of the burgeoning protein chip market. 

Obviously, I may be a bit biased on this topic.