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Proteomics

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...

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Related Experiment Video

Updated: Jul 18, 2025

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

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

Published on: November 15, 2017

Serial and multi-level proteome analysis for microscale protein samples.

Dongying Huang¹, Yeye Leng¹, Xiangye Zhang²

¹School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China.

Journal of Proteomics

|August 24, 2023

Summary

This summary is machine-generated.

Researchers developed a new microscale strategy for multi-level proteome analysis, enabling comprehensive study of post-translational modification crosstalk. This method efficiently profiles total proteome, ubiquitinome, and phosphoproteome from small samples.

Keywords:

PTM crosstalk Phosphorylation Serial enrichment Ubiquitination

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Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

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Published on: April 1, 2017

Area of Science:

Proteomics
Biochemistry
Molecular Biology

Background:

Post-translational modifications (PTMs) like phosphorylation and ubiquitination are crucial for cellular signaling and protein regulation.
Understanding the crosstalk between different PTMs is essential for comprehending complex biological systems.
Existing multi-level proteome analysis methods are often technically challenging and require large sample amounts.

Purpose of the Study:

To develop a robust and efficient strategy for multi-level proteome analysis using microscale starting material.
To enable serial profiling of the total proteome, ubiquitinome, and phosphoproteome.
To investigate the crosstalk between ubiquitination and phosphorylation in biological samples.

Main Methods:

Evaluation of lysis buffers to identify optimal conditions for multi-level proteome analysis.
Development of a serial enrichment approach for sequential isolation of ubiquitinome and phosphoproteome.
Customization of variable windows for data-independent acquisition (DIA) sequencing to enhance identification depth.

Main Results:

Sodium deoxycholate buffer demonstrated superior performance for multi-level proteome analysis.
Sequential enrichment of ubiquitinome and phosphoproteome maintained reproducibility.
Identification of 6465 proteins, ~20,000 GlyGly sites, and ~19,000 phosphosites from 1 mg of HeLa digest using three DIA measurements.
Observed crosstalk between ubiquitination and phosphorylation in MG132-treated HeLa cells.

Conclusions:

The developed strategy enables comprehensive multi-level proteome analysis from microscale samples.
This method provides a valuable tool for studying PTM crosstalk and its biological implications.
The findings offer a reference for future multi-level proteome studies, particularly with limited sample availability.