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Related Concept Videos

Proteomics01:33

Proteomics

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 proteomics...
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...

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Related Experiment Video

Updated: Jun 6, 2026

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis
07:44

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis

Published on: June 8, 2020

Time series proteome profiling.

Catherine A Formolo1, Michelle Mintz, Asako Takanohashi

  • 1Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC, USA.

Methods in Molecular Biology (Clifton, N.J.)
|November 18, 2010
PubMed
Summary
This summary is machine-generated.

This study details a method to track endoplasmic reticulum (ER) proteome changes in cells under stress. It uses SILAC labeling and mass spectrometry to identify proteins altered by tunicamycin or thapsigargin treatment.

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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

Related Experiment Videos

Last Updated: Jun 6, 2026

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis
07:44

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis

Published on: June 8, 2020

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
10:37

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

Area of Science:

  • Proteomics
  • Cell Biology
  • Biochemistry

Background:

  • The endoplasmic reticulum (ER) is crucial for protein homeostasis.
  • ER stress can lead to various cellular dysfunctions and diseases.
  • Understanding temporal proteome dynamics during ER stress is vital.

Purpose of the Study:

  • To describe a method for analyzing temporal proteome alterations in the ER.
  • To investigate changes in fibroblast cell proteomes upon exposure to ER stress agents.
  • To quantify differential protein expression under tunicamycin and thapsigargin treatment.

Main Methods:

  • Differential stable isotope labeling by amino acids in cell culture (SILAC) for quantitative proteomics.
  • Crude ER fractionation to isolate the endoplasmic reticulum proteome.
  • SDS-PAGE and LC-MS/MS for protein separation and peptide analysis.
  • Bioworks and Swiss-Prot for protein identification, and ZoomQuant for quantification.

Main Results:

  • Identification of proteins with altered expression levels in ER-stressed cells.
  • Quantification of protein ratio changes between treated and untreated cell populations.
  • Temporal profiling of proteomic responses to specific ER stress inducers.

Conclusions:

  • The described method enables detailed temporal analysis of the ER proteome during stress.
  • This approach facilitates the identification of key proteins involved in ER stress response pathways.
  • The findings contribute to a better understanding of cellular mechanisms underlying ER stress.