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Proteomics01:33

Proteomics

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
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The mammalian target of rapamycin  (mTOR) is a serine/threonine kinase that regulates growth, proliferation, and cell survival in response to hormones, growth factors, or nutrient availability. This kinase exists in two structurally and functionally distinct forms: mTOR complex 1  (mTORC1) and mTOR complex 2  (mTORC2). The first form (mTORC1) is composed of a rapamycin-sensitive Raptor and proline-rich Akt substrate, PRAS40. In contrast,  mTORC2 consists of a...
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Related Experiment Video

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Quantitative Mass Spectrometric Profiling of Cancer-cell Proteomes Derived From Liquid and Solid Tumors
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Quantitative Top-down Proteomics Revealed Kinase Inhibitor-Induced Proteoform-Level Changes in Cancer Cells.

Trishika Chowdhury1, Kellye A Cupp-Sutton1, Yanting Guo2

  • 1Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35401, United States.

Journal of Proteome Research
|December 2, 2024
PubMed
Summary
This summary is machine-generated.

A new high-throughput top-down proteomics platform quantifies intact proteoforms and their modifications. This method revealed significant changes in catabolic, metabolic, and apoptotic pathways after kinase inhibitor treatment in HeLa cells.

Keywords:
LC−MS/MSTop-down proteomicskinase inhibitionphosphoproteomicsquantitative proteomics

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Area of Science:

  • Proteomics
  • Cellular Biology
  • Biochemistry

Background:

  • Quantitative analysis of proteins and post-translational modifications (PTMs) is crucial for understanding cellular processes and disease.
  • Top-down proteomics offers a comprehensive view of the proteome by analyzing intact proteoforms.

Purpose of the Study:

  • To develop a high-throughput quantitative top-down proteomics platform.
  • To investigate changes in intact proteoform and phosphoproteoform abundance in HeLa cells treated with staurosporine (STS), a kinase inhibitor.

Main Methods:

  • Development of a high-throughput quantitative top-down proteomics platform.
  • Analysis of HeLa cells treated with staurosporine (STS).
  • Identification and quantification of proteoforms and phosphoproteoforms.

Main Results:

  • 1187 proteoforms from 215 families were identified and quantified.
  • 55 proteoforms from 37 families showed significant changes upon STS treatment, primarily in catabolic, metabolic, and apoptotic pathways.
  • Differential regulation of phosphorylated versus unphosphorylated proteoforms within the same family was observed, exemplified by eukaryotic initiation factor 4E binding protein 1 (4EBP1).

Conclusions:

  • The developed platform enables high-throughput quantitative analysis of intact proteoforms and their PTMs.
  • Top-down proteomics provides a more comprehensive understanding of cellular responses to kinase inhibition than bottom-up methods.
  • Differential regulation of proteoforms and phosphoproteoforms offers insights into complex cellular signaling pathways.