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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: Jan 11, 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

Comparative Analysis of Proteoform Clean-Up Methods for In-Depth Top-Down Proteomics.

Alyssa A Williams¹, Kendalyn N Firenza², Amy K Carfagno¹

¹School of Biological Sciences, University of Oklahoma, Norman, Oklahoma, USA.

|November 10, 2025

Summary

This summary is machine-generated.

Top-down proteomics (TDP) benefits from efficient sodium dodecyl sulfate (SDS) removal. This study benchmarks commercial kits against methanol-chloroform-water (MCW) precipitation, finding Minute SDS offers broad proteome coverage at a lower cost.

Keywords:

PEPPI‐MS detergent removal proteomics sample preparation top‐down mass spectrometry

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Last Updated: Jan 11, 2026

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

Published on: November 15, 2017

Area of Science:

Biochemistry
Analytical Chemistry
Proteomics

Background:

Proteoforms, encompassing genetic and post-translational variations, are crucial for understanding biological mechanisms and disease.
Top-down proteomics (TDP) analyzes intact proteoforms, often requiring sodium dodecyl sulfate (SDS) for fractionation.
Efficient SDS removal is critical as it interferes with mass spectrometry analysis.

Purpose of the Study:

To benchmark four commercial SDS clean-up kits against traditional methanol-chloroform-water (MCW) precipitation for TDP.
To evaluate SDS removal efficiency, proteoform recovery, post-translational modification (PTM) retention, and ease of use.
To provide practical guidance for optimizing TDP sample preparation workflows.

Main Methods:

Comparison of four commercial SDS clean-up kits (DetergentOUT, HiPPR, Minute SDS, SurfactAway) with methanol-chloroform-water (MCW) precipitation.
Assessment of SDS removal efficacy using mass spectrometry-based techniques.
Evaluation of proteoform identification numbers, focusing on recovery of small and acidic proteoforms.
Analysis of PTMs, particularly methylation, across different clean-up methods.

Main Results:

MCW precipitation resulted in fewer proteoform identifications, especially for small and acidic proteoforms.
Commercial kits DetergentOUT and HiPPR showed SDS removal comparable to MCW but at a higher cost.
Minute SDS and SurfactAway kits enabled the identification of a higher number of proteoforms.
Increased prevalence of methylation modifications was observed post-MCW clean-up.

Conclusions:

For studies sensitive to the loss of low molecular weight or acidic proteoforms, commercial kits like DetergentOUT and HiPPR may offer advantages.
Minute SDS provides a cost-effective alternative with sufficient SDS removal and broader proteome coverage.
These findings support the development of more streamlined, reproducible, and accessible TDP workflows for biological and clinical research.