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Related Experiment Video

Updated: Oct 8, 2025

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis

Published on: June 8, 2020

Studying Autophagy Using a TMT-Based Quantitative Proteomics Approach.

Kiran Bala Sharma¹, Suruchi Aggarwal², Amit Kumar Yadav²

¹Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India.

Methods in Molecular Biology (Clifton, N.J.)

|January 1, 2022

Summary

This summary is machine-generated.

Autophagy, a key cellular process, is studied using tandem mass tag (TMT)-based mass spectrometry (MS) proteomics. This method reveals how autophagy dysfunction impacts cellular proteomes during conditions like viral infection.

Keywords:

ATG5 Autophagy Mass spectrometry Quantitative proteomics TMT

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Last Updated: Oct 8, 2025

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis

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Published on: June 8, 2020

Quantitative Analysis of Autophagy using Advanced 3D Fluorescence Microscopy

Quantitative Analysis of Autophagy using Advanced 3D Fluorescence Microscopy

Published on: May 3, 2013

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Published on: November 13, 2021

Area of Science:

Cell Biology
Biochemistry
Proteomics

Background:

Autophagy maintains cellular homeostasis by degrading proteins and organelles.
The ATG protein family tightly regulates autophagy.
Perturbing autophagy significantly alters cellular proteomes and biological processes.

Purpose of the Study:

To provide a protocol for studying autophagy perturbations using quantitative proteomics.
To investigate the impact of dysfunctional autophagy on cellular proteomes and pathways.
To compare healthy versus disease (virus infection) conditions.

Main Methods:

Utilizing a 16-plex tandem mass tag (TMT)-based mass spectrometry (MS) quantitative proteomics approach.
Applying a data processing and analysis pipeline with web-based tools.
Examining relative protein abundances across multiple samples.

Main Results:

Global proteome quantification to understand autophagy-regulated processes.
Identification of protein-protein interaction networks and spatiotemporal dynamics.
Discovery of novel autophagy substrates.

Conclusions:

TMT-based MS proteomics is a powerful tool for global autophagy research.
This approach offers insights into cellular responses to autophagy dysfunction.
The protocol facilitates the study of autophagy in health and disease states.