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Chapter 49: Problem 7

What are the approaches used in the development of clinical proteomics?

Short Answer

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In conclusion, clinical proteomics plays a critical role in understanding the protein composition and functionality in biological systems, subsequently aiding in the identification of biomarkers and therapeutic targets for diseases. Key approaches in clinical proteomics include mass spectrometry-based proteomics, two-dimensional gel electrophoresis, differential in-gel electrophoresis, protein microarrays, and protein-protein interaction networks. These methods provide valuable insights into protein identification, quantification, expression, interactions, and activities, ultimately contributing to our understanding of disease processes and potential therapeutic interventions.

Step by step solution

01

Introduction to Clinical Proteomics

In clinical proteomics, the primary focus is on understanding the protein composition and functionality in biological systems to identify biomarkers and therapeutic targets for diseases. Different approaches are employed to study proteins and their role in disease processes. The following are some of the main approaches used in clinical proteomics.
02

Mass Spectrometry-based Proteomics

Mass spectrometry (MS) is a widely used method in proteomics, providing a means of identifying and quantifying proteins within a specific sample. Through various techniques such as liquid chromatography-tandem mass spectrometry (LC-MS/MS) and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF), researchers can analyze complex protein mixtures, map post-translational modifications, and determine protein interactions with high precision, sensitivity, and speed.
03

Two-Dimensional Gel Electrophoresis

In two-dimensional gel electrophoresis (2-DE), proteins are first separated based on their isoelectric points in the first dimension using isoelectric focusing (IEF). Then, the proteins are further separated based on their molecular weights using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in the second dimension. This method enables the visualization and comparison of protein expression levels between different samples, such as healthy and diseased tissues.
04

Differential in-Gel Electrophoresis

Differential in-gel electrophoresis (DIGE) is an improved version of two-dimensional gel electrophoresis, utilizing fluorescent dyes to label proteins from different samples. These samples are run simultaneously on the same gel, reducing gel-to-gel variations and improving the identification of differentially expressed proteins.
05

Protein Microarrays

Protein microarrays are high-throughput platforms where thousands of proteins can be immobilized on a solid surface in an ordered array. They enable large-scale studies on protein-protein, protein-DNA, or protein-small molecule interactions, and facilitate the identification of disease-associated proteins. There are two primary types of protein microarrays: analytical microarrays (used for identifying protein interactions) and functional microarrays (used for detecting protein activities).
06

Protein-Protein Interaction Networks

Analyzing protein-protein interaction (PPI) networks provides insights into the biological pathways and functional modules involved in disease-related processes. Technologies such as yeast two-hybrid systems, protein complementation assays, and co-immunoprecipitation are employed to investigate these interactions. Computational methods can then be used to model and analyze PPI networks further, helping to identify novel therapeutic targets. These mentioned approaches outline the primary methods used in the development of clinical proteomics, each offering unique information about proteins and their roles in health and disease.

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Most popular questions from this chapter

Top-down approach in studies of systems biology is preferential over bottom-up approach because: a. it provides more global view b. it allows for faster conclusions which will lead to direct development of clinical tests c. requires less sophisticated technology and instrumentation d. both approaches are equal

Weakness of 2-dimensional SDS-PAGE is: a. lack of superior reproducibility b. lack of protection of proteins from structural destabilization c. inability of obtaining protein sequencing data d. lack of superior methods of protein labeling

While planning proteomics experiments, a researcher should: a. have available all types of mass spectrometers b. mandatory access to protein microarrays c. be aware of strength and weaknesses of each technology d. always be an expert in statistics and computer programming for solving problems associated with bioinformatics

Explain in which cases SELDI-TOF technology will be more advantageous than LC- MS/MS and/or MALDI-TOF.

What are biomarkers and how are they identified and validated for use in the clinical setting?
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