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- Read one or more of the target protein(s) retained by a rapid, sensitive,
laser- induced process (SELDI) that provides direct information about the target
(molecular weight). - Process (characterize) the target protein(s) at any one or more locations within
the addressable array directly in situ by engaging in one or more on-the-chip
binding or modifi cation reactions to characterize protein structure and function.
Software produces map of proteins, revealing expression of marker protein with
color change in the patient sample as compared to the control sample.
The ProteinChip system uses small arrays or plates with chemically or biologi-
cally treated surfaces to interact with proteins. Unknown proteins are affi nity cap-
tured on treated surfaces, desorbed and ionized by laser excitation, and detected
according to molecular weight. Known proteins are analyzed using on-chip func-
tional assays. For example, chip surfaces can contain enzymes, receptor proteins or
antibodies, enabling on-chip protein-protein interaction studies, ligand binding
studies or immunoassays. With state-of-the-art ion optic and laser optic technolo-
gies, the ProteinChip System detects proteins ranging from small peptides of less
than 1,000 Da up to proteins of 300 kDa or more and calculates the mass based on
time-of-fl ight. The system includes ProteinChip arrays and reagents consumed in
the process, the chip reader, software to analyze results and proprietary database to
enable comparison between phenomic and genomic data. New ProteinChip Arrays
have been packaged into a series of application-specifi c kits to enhance ease-of-use
for the biologist performing protein analysis. ProteinChip Biomarker System
enables clinical researchers to rapidly discover, characterize and validate predictive
protein biomarkers and biomarker patterns in their own laboratories.
ProteinChip “benchtop” system and Tandem MS system have several advantages
over the 2-D gel method. These include speed of detection (hours versus days),
coverage of a broader region of the proteome, small sample requirement (1 ml or
500 cells) and combination of discovery and assay in a single system. An example
of this is the discovery of prostate cancer biomarkers. With ProteinChip technology,
it is possible to discriminate between benign prostatic hypertrophy with bound PSA
(prostate-specifi c antigen) and cancer of the prostate with free PSA.
LumiCyte (a subsidiary of QIAGEN) has integrated SELDI with artifi cial
intelligence- based data analysis capabilities and a powerful bioinformatics interro-
gation platform. Unlike other molecular mapping technologies, and protein bio-
marker detection assays designed to reveal disease, the SELDI BioChip molecular
profi ling platform enables both discovery and routine assays to be performed on the
same BioChip in the same unit operation.
Proteomic Pattern Analysis
Proteomic pattern analysis might ultimately be applied as a screening tool for
cancer in high-risk and general populations. This also applies to autoimmune dis-
eases, by screening sera of patients or high-risk individuals for the presence of
2 Molecular Diagnostics in Personalized Medicine