Applications of Mass-Spectrometry Based Quantitative Proteomics to Understand Complex Cellular Functions and Cell Fate Decisions
Journal Title: Biomedical Journal of Scientific & Technical Research (BJSTR) - Year 2017, Vol 1, Issue 1
Abstract
Unlike the transcriptome, quantification of the proteome still requires the development of special strategies. Transcriptomics platforms such as microarray- and RNAseq-based approaches are designed to uncover the information at the transcriptome level that in turn shapes the proteome to carry out the functional cellular processes. Since most of the biological processes are controlled by proteins, it is important to quantitatively measure proteome alterations in varying conditions to mechanistically understand how cellular processes are carried out. Within the last decade mass spectrometry increasingly became the method of choice for proteome analyses and now also provides a solid platform for its accurate quantification. The aim of quantitative proteomics is to obtain reliable quantitative information about all the proteins that fall within the mass spectrometric dynamic range. Protein analysis is often performed by conventional techniques such as staining of gel-separated proteins or antibody-based methods. With the emergence of the post-genomic and systems biology era there is a paradigm shift from targeted studies involving specific proteins to a more global proteome analysis encompassing all proteins expressed in a certain condition (“omics approach”). Such large scale or global proteomic studies aim at the identification and quantification of altered biological pathways of entire cellular systems in the chosen experimental condition with an unbiased approach. For accurate characterization of the proteome mass spectrometry (MS) is the method of choice since this technique provides molecular specificity and high sensitivity [1]. The advent of MALDI (matrix-assisted laser desorption/ ionization) and ESI (electrospray ionization) made it possible to use biomolecules such as peptides for mass spectrometric analysis. For these two methodic innovations the Nobel Prize in Chemistry was awarded in 2002. The combination of liquid chromatography (LC) with ESI and tandem MS (LC-MS/MS) is a highly efficient technique to deal with complex samples such as digested protein mixture obtained from a cell or tissue lysate. The general workflow of a typical mass spectrometry-based proteomics analysis is depicted in (Figure 1). The masses and the corresponding fragment ion spectra of the peptides are assigned to known protein sequences by searching a protein sequence database. Development of computational platforms such as Max Quant [2] along with the built in database search engine called Andromeda [3] has automatized protein identification and quantification by LC-MS/MS.
Authors and Affiliations
Sajib Chakraborty, Hossain Uddin Shekhar
Keywords
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- EP ID EP567448
- DOI 10.26717/BJSTR.2017.01.000144
- Views 197
- Downloads 0
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