# Proteomics/Protein Chips

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**Introduction:** \_\_TOC\_\_

## Introduction

!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.

## History

### 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. 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., 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

## References

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Chapter written by: Jonathan Keeling and Eric Foster\
Contact jwk3970@rit.edu, edf3480@rit.edu, ttl5439@rit.edu\


[^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
    \<<http://en.wikipedia.org/wiki/Affymetrix>\>
