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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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Updated: Mar 25, 2026

Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry

Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry

Published on: October 24, 2018

A Method for Label-Free, Differential Top-Down Proteomics.

Ioanna Ntai^1,2,3, Timothy K Toby^1,2,3, Richard D LeDuc^1,2,3

¹Department of Chemistry, Northwestern University, Evanston, IL, USA.

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

|February 13, 2016

Summary

This summary is machine-generated.

This study introduces a novel label-free, high-throughput top-down proteomics method for whole protein characterization and quantitation. This approach advances biomarker discovery in translational research by analyzing intact proteins without labeling.

Keywords:

Differential expression Label-free quantitation Proteoform Quantitative mass spectrometry Top-down proteomics Top-down quantitation

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Area of Science:

Proteomics
Biomarker Discovery
Mass Spectrometry

Background:

Biomarker discovery in translational research traditionally relies on quantitative bottom-up proteomics.
Existing methods often require metabolic or chemical labeling, complicating the process.
There is a need for methods that offer whole protein characterization and relative quantitation simultaneously.

Purpose of the Study:

To present a novel high-throughput top-down proteomics approach for biomarker studies.
To enable whole protein characterization and relative quantitation in a single experiment.
To develop a label-free method for quantifying intact proteins.

Main Methods:

Utilized high-throughput top-down proteomics.
Developed a label-free quantitative approach for intact proteins (0-30 kDa) using yeast as a model.
Employed liquid chromatography-mass spectrometry (LC-MS) for large-scale proteome profiling and quantitation.
Implemented a robust sample preparation workflow and a hierarchical linear statistical model for variance analysis.

Main Results:

Successfully demonstrated a label-free method for quantifying the relative abundance of intact proteins.
Achieved whole protein characterization and relative quantitation within the same experiment.
Validated the methodology on yeast proteomes, showing its applicability for proteins up to 30 kDa.

Conclusions:

The developed quantitative top-down proteomics approach offers a powerful, label-free alternative for biomarker discovery.
This integrated methodology facilitates large-scale profiling and quantitation of the intact proteome.
The method is suitable for basic and clinical research, providing robust quantitation of proteomic comparisons.