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Related Experiment Video

Updated: Feb 19, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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MSE for Label-Free Absolute Protein Quantification in Complex Proteomes.

Stefan Helm1, Sacha Baginsky2

  • 1Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Weinbergweg 22, 06120, Halle (Saale), Germany.

Methods in Molecular Biology (Clifton, N.J.)
|November 1, 2017
PubMed
Summary
This summary is machine-generated.

This study introduces MSE, a label-free peptide quantification method for analyzing proteome dynamics. It offers accurate protein quantification in complex samples, even with limited data, and improves identification sensitivity with ion mobility.

Keywords:
In solution digestIon mobility separationLabel-free quantificationMSEProteome analysis

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Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biochemistry

Background:

  • Label-free peptide quantification enables cost-effective proteome dynamics analysis.
  • Existing methods like spectral counting often require large datasets for robust quantification.

Purpose of the Study:

  • To describe an absolute label-free quantification method using MSE (Mass Spectrometry) fragmentation.
  • To evaluate the accuracy and sensitivity of this method, especially when combined with ion mobility separation.
  • To provide guidance on optimizing sample loading and data interpretation for reliable protein quantification.

Main Methods:

  • Utilized an untargeted peptide fragmentation approach termed MSE.
  • Incorporated ion mobility separation into the liquid chromatography-mass spectrometry (LC-MS) workflow.
  • Employed spiked external standards for absolute quantification in complex samples.

Main Results:

  • MSE achieved quantification accuracy comparable to spectral counting, particularly for smaller sample sets.
  • Ion mobility significantly enhanced protein identification sensitivity by reducing sample complexity.
  • Detector saturation was identified as a limitation for high-abundance proteins, necessitating optimized workflows.

Conclusions:

  • MSE provides a robust and sensitive method for label-free protein quantification, especially when coupled with ion mobility.
  • Optimizing sample loading (400-600 ng) is crucial for accurate identification and quantification.
  • The method demonstrates a dynamic range of 3-4 orders of magnitude for complex samples up to 2000-3000 proteins.