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Proteomics/Protein Chips


Protein - Protein Interactions
Protein Chips
Proteomics and Drug Discovery
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Proteomics and Drug Discovery


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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.[1] 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.


Nucleic Acid Microarrays

The use of microarrays for gene expression profiling was first published in 1995.[2] This technology allowed scientists to analyze thousands of mRNAs in a single experiment to determine whether expression is different in disease states. Unfortunately, mRNA levels within a cell are often poorly correlated with actual protein abundance.[3] This can be due to many factors including degradation rate of mRNA versus proteins and post-transcriptional controls and modifications. Measuring the amount of protein directly would bypass any mRNA inconsistencies and give a true level of gene function, however traditional protein characterization methods were slow and cumbersome. These combined factors were the impetus behind the creation of protein chips.

Deficiency of Traditional Protein Characterization Methods

A liquid chromatography / mass spectrometry (LC/MS) instrument. This technique is low throughput compared to protein chips because protein chips can test for thousands of proteins on a single chip in a single experiment.

Before the advent of protein chips, protein measuring and characterization was done using two different methods: 2D gel electrophoresis coupled with mass spectrometry, and liquid chromatography. These methods can separate and visualize a large number of proteins per experiment, however they are time consuming when compared to protein chips. Their process is very low-throughput because of lack of automation. Reproducibility is also a factor because of the large amount of sample handling. A better, more standardized, higher-throughput method needed to be invented for protein measuring and characterization.

Protein Chip Precursors to Modern Day

The equipment and reagents used in an Enzyme-linked Immunosorbent Assay (ELISA), a precursor of protein chips.

Immunoassays, the precursor to protein chips available since the 1980s, exploit the interactions between antibodies and antigens in order to detect their concentrations in biological samples. Their creation, however, is tedious and expensive. As a response to this, researchers at Harvard University combined the technologies of immunoassays and DNA microarrays to develop the protein chip.[4] In their landmark paper, published in 2000, "Printing Proteins as Microarrays for High-Throughput Function Determination," Gavin MacBeath and Stuart Schreiber described how to create protein chips and demonstrated three types of applications that would benefit from this new technology. The strengths of their approach were the use of readily available materials (i.e. glass slides, polyacrylamide gel), the relative ease of implementation (robotic microarray printers), and compatibility with standard instrumentation.

Within the past five years, many companies, including Biacore, Invitrogen, and Sigma-Aldrich, have begun production of industrial level protein array systems that can be used for drug discovery and basic biological research. Commercial entities have made protein chip research a streamlined and standardized process on the same level as DNA microarrays compared to its inception in 2000.

Academic research plays a huge role in the development and improvement of these technologies. The collaboration of academic research with systems such as the Affymetrix GeneChip and the Human Genome Initiative has allowed for friendly competition, resulting in the advancement of technologies. With more develops come a better understanding and encourages even more research towards these fields.

Affymetrix is a company that has been manufactures microarrays, named GeneChip, since 1992. They have 13 locations across the world with headquarters located in the US (California), UK, Japan, and China.[5]

Next section: Manufacture


  1. MacBeath G, Schreiber S. (2000). Printing Proteins as Microarrays for High-Throughput Function Determination. Science. Sep 08; 289 (5485): 1760-1764.
  2. Schena M, Shalon D, Davis RW, Brown PO. (1995). Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. Oct 20; 270 (5235): 467-70.
  3. Gygi SP, Rochon Y, Franza B, Abersold R: Correlation between protein and mRNA abundance in yeast. Mol. Cell Biol. 19, 1720-1730 (1999).
  4. MacBeath G, Schreiber S. (2000). Printing Proteins as Microarrays for High-Throughput Function Determination. Science. Sep 08; 289 (5485): 1760-1764.
  5. "Affymetrix." Wikipedia, The Free Encyclopedia. 5 Feb 2007, 03:19 UTC. Wikimedia Foundation, Inc. Apr 2008 <>

Chapter written by: Jonathan Keeling and Eric Foster