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Related Concept Videos

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.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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Related Experiment Video

Updated: Oct 28, 2025

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
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SILIA-Based 4C Quantitative PTM Proteomics.

Emily Oi Ying Wong1,2, Ning Li3,4

  • 1Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, SAR, China.

Methods in Molecular Biology (Clifton, N.J.)
|July 16, 2021
PubMed
Summary
This summary is machine-generated.

This study introduces SILIA-based 4C quantitative PTM proteomics (S4Quap) for precisely measuring changes in post-translationally modified (PTM) proteomes. This method enables accurate quantification of PTM alterations in response to various signals.

Keywords:
15N-Stable isotope labeling in Arabidopsis (SILIA)Double in vivo substrate and kinase assay (DISKA)Functional validationPosttranslational modification (PTM)SILIA-based 4C quantitative PTM proteomics (S4Quap)SILIQUE-N/SQUA-N

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Area of Science:

  • Proteomics
  • Biochemistry
  • Plant Science

Background:

  • Post-translational modifications (PTMs) are crucial for protein function and cellular signaling.
  • Quantifying PTM alterations in response to stimuli is essential for understanding biological processes.
  • Existing methods may lack the precision or scope for comprehensive PTM analysis.

Purpose of the Study:

  • To develop and validate a novel quantitative proteomics approach for PTM analysis.
  • To enable absolute and relative quantification of PTM proteome alterations.
  • To investigate PTM changes in response to specific internal or external signals in plants.

Main Methods:

  • Integration of 15N-stable isotope labeling in Arabidopsis (SILIA) with 4C quantitative PTM proteomics (S4Quap).
  • Utilized urea-based extraction buffer (UEB) for efficient plant protein isolation and denaturation.
  • Employed affinity enrichment, ion exchange chromatography, and LC-MS/MS for PTM peptide analysis.
  • Applied target-decoy analysis, extracted ion chromatogram (XIC) ratio analysis, and Benjamini-Hochberg (BH) correction for statistical validation.

Main Results:

  • The S4Quap method allows for precise quantification of PTM proteome alterations.
  • Successfully identified and quantified differentially regulated PTM peptides using SILIA and 4C approaches.
  • Established a robust workflow for PTM analysis with high statistical confidence (BH-FDR < 5%).

Conclusions:

  • S4Quap provides a powerful tool for quantitative PTM proteomics in plants.
  • This method facilitates the identification and validation of key PTM proteins involved in signaling pathways.
  • The approach is broadly applicable for studying PTM dynamics in various biological contexts.