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Related Experiment Video

Updated: May 28, 2026

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

MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics.

Lily Ting¹, Ramin Rad, Steven P Gygi

¹Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.

|October 4, 2011

Summary

This summary is machine-generated.

Triple-stage mass spectrometry (MS3) effectively minimizes protein quantification interference in multiplexed proteome analysis. This advancement improves the accuracy of quantitative proteomics, especially when analyzing complex biological samples.

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Published on: May 1, 2017

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Last Updated: May 28, 2026

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

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Enhanced Sample Multiplexing of Tissues Using Combined Precursor Isotopic Labeling and Isobaric Tagging (cPILOT)

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Published on: May 1, 2017

Area of Science:

Proteomics
Mass Spectrometry
Analytical Chemistry

Background:

Quantitative mass spectrometry is a powerful proteomics tool but lacks easy multiplexing capabilities.
Isobaric labeling enables multiplexed proteome quantification but suffers from ratio distortion due to interference.
Protein quantification interference is a significant challenge in multiplexed mass spectrometry-based proteomics.

Purpose of the Study:

To investigate and quantify the interference effect in a sixplex isobaric labeling system.
To evaluate the efficacy of triple-stage mass spectrometry (MS3) in mitigating interference.
To establish a robust method for accurate multiplexed proteome quantification.

Main Methods:

Development of a two-proteome model using a mixture of human and yeast proteins.
Application of a sixplex isobaric labeling strategy for sample preparation.
Utilizing triple-stage mass spectrometry (MS3) for enhanced data acquisition.

Main Results:

The study successfully documented the interference effect in a sixplex isobaric labeling system.
Triple-stage mass spectrometry (MS3) was found to almost completely eliminate the observed interference.
Accurate proteome quantification was achieved by mitigating ratio distortion.

Conclusions:

Triple-stage mass spectrometry (MS3) is a highly effective solution for overcoming protein quantification interference in isobaric labeling-based proteomics.
This method significantly enhances the reliability and accuracy of multiplexed proteome quantification.
The findings pave the way for more precise and comprehensive proteomic analyses.