Proteomics: Decoding functions

The term “proteomics” was first used by Marc Wilkins in 1996 to denote the “PROTein complement of a genOME”.The functional information of genes is characterized by the proteome. Proteomics also deals with characterization of proteome which includes expression, structure, interactions and modifications of proteins at any stage. . Thus, the proteomics would be considered as the most relevant data set to characterize a biological system.

Fluctuations in gene expression level can be determined by analysis of transcriptome to discriminate between two biological states of the cell. Microarray chips are used for large-scale analysis of whole transcriptome. However, increase synthesis of mRNA cannot measure directly by microarray. Proteins which are effectors of biological function and their levels are not only dependent on corresponding mRNA levels but also on host translational control and regulation

Techniques to determine proteomics:

A) Conventional Techniques:

  • The conventional techniques for purification of proteins are chromatography based such as ion exchange chromatography (IEC), size exclusion chromatography (SEC) and affinity chromatography.
  • For analysis of selective proteins, enzyme-linked immunosorbent assay (ELISA) and western blotting can be used.
  • Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), two-dimensional gel electrophoresis (2-DE) and two-dimensional differential gel electrophoresis (2D-DIGE) techniques are used for separation of complex protein samples.

B) Advanced Techniques:

  • The diverse proteomics approaches such as mass spectrometry (MS) have developed to analyze the complex protein mixtures with higher sensitivity.
  • Additionally, Edman degradation has been developed to determine the amino-acid sequence of a particular protein.

C) Qualitative Techniques:

  • Isotope-coded affinity tag (ICAT) labeling, stable isotope labeling with amino acids in cell culture (SILAC) and isobaric tag for relative and absolute quantitation (iTRAQ) techniques have recently developed for quantitative proteomic.

D)High-throughput techniques:

  • X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy are two major high-throughput techniques that provide three-dimensional (3D) structure of protein that might be helpful to understand its biological function.

E) Bioinformatics Techniques:

  • Various bioinformatics tools are developed for 3D structure prediction, protein domain and motif analysis, rapid analysis of protein–protein interaction and data analysis of MS and the alignment tools are helpful for sequence and structure alignment to discover the evolutionary relationship.

Applications:

  • Proteomics is crucial for early disease diagnosis, prognosis and to monitor the disease development.
  • Proteomics is used for various procedures to detect diagnostic markers, candidates for vaccine production, alteration of expression patterns in response to different signals, understanding pathogenicity mechanisms, and interpretation of functional protein pathways in different diseases.
  • The combination of proteomics with other experimental approaches in biochemistry, cell biology, molecular cancergenomics and chemistry, together with the development of new technologies and improvements in existing methodologies will continue to extend its application in studying cancer metastasis.
  • Proteomics, with its high-throughput and unbiased approach to the analysis of variations in protein expression patterns (actual phenotypic expression of genetic variation), promises to be the most suitable platform for biomarker discovery.

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