A DNA microarray as seen through a microscope. Protein chips look identical, except each spot corresponds to one of the organism’s thousands of proteins, instead of one of it’s genes. The intensity of the dot indicates the amount of protein present.
Protein chips, also referred to as protein arrays or protein microarrays, are modeled after DNA microarrays. The success of DNA microarrays in large-scale genomic experiments inspired researchers to develop similar technology to enable large-scale, high-throughput proteomic experiments. Protein chips enable researchers to quickly and easily survey the entire proteome of a cell within an organism. They also allow researchers to automate and parallelize protein experiments.
Protein chips were first developed in 2000 by researchers at Harvard University. Today there are many companies manufacturing protein chips using many types of techniques including spotting and gel methods. The types of protein chips available include “lab on a chip”, antibody arrays and antigen arrays, as well as a wide range of chips containing “alternative capture agents” such as proteins, substrates and nucleic acids.
Analysis of protein chips comes with many challenges including dynamic protein concentrations, the sheer number of proteins in a cell’s proteome, and the understanding of the probes for each protein. Steps include the reading of the protein levels off the chip, and then the use of computer software to analyze the massive amounts of data collected.
Applications of protein chip experiments include identifying biomarkers for diseases, investigating protein-protein interactions, and testing for the presence of antibodies in a sample. Protein chips have applications in cancer research, medical diagnostics, homeland security and proteomics.
This chapter will demonstrate why protein chips are changing the face of proteomics, and why they will have an even larger impact in the future.