L8_Proteomics - ECEN 689 Statistical Computation in GSP

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Unformatted text preview: ECEN 689 Statistical Computation in GSP http://www.ece.tamu.edu/~ulisses/ECEN689/ Lecture 8: Proteomics and Mass Spectrometry Ulisses Braga-Neto Genomic Signal Processing Laboratory Department of Electrical and Computer Engineering Texas A&M University What is Proteomics? Proteomics involves the identification and quantitation of peptides/proteins present in serum or other circulating fluids in the body. There may be poor correlation between mRNA concentrations and the corresponding protein, due to post-translational modifications. Proteomics avoids this issue by measuring directly the final product of gene expression. Open or probe-free" measurement technologies are more suitable for Proteomics, given the complexity of the (human) proteome. Proteomics often involves biomarker discovery. Biomarker Discovery There is intense interest among clinicians, pharmaceutical companies, and the governement in obtaining fast and accurate diagnostics methods based on proteomics. This typically involves the discovery and clinical validation of peptide biomarkers in the blood serum. One famous example of peptide biomarker is prostate specific antigen (PSA), a marker for the early diagnosis of prostate cancer in men. Biomarker Discovery - II As of 2008, PSA is the only FDA-approved serum or plasma-based population screening tool for any cancer. The specificity of this biomarker is low; only 25-30% of men with elevated PSA (>7.0 ng/ mL) have prostate cancer on biopsy. The poor specificity of PSA leads to an annual cost of $750 million in unnecessary medical follow-up. PSA illustrates the challenge of proteomics for biomarker discovery, and the need for powerful techniques and careful analysis. Measurement Technologies The main high-throughput technologies for proteomics are: Microarrays (closed) Antibody Microarrays Peptide Microarrays 2-D Gel Electrophoresis (open) Mass Spectrometry (open) Antibody Microarrays Antibody microarrays consist of antibody probes and antigen peptide targets. Hence, they can be used to measure concentrations of antigen peptides for which the antibody probes are complementary. Such microarrays have been used for example in the proteomic profiling of cancer antigens. One of the main drawbacks of this approach is that it requires the production of speciFc antibody sets for each of the antigen targets. Peptide Microarrays Peptide microarrays use the opposite technical approach; that is, they use antigen peptides as probes and antibodies as targets. Peptide microarrays can be used for studying enzyme specificities and protein interactions....
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L8_Proteomics - ECEN 689 Statistical Computation in GSP

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