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Related Experiment Video

Updated: Nov 25, 2025

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Highly Multiplexed Targeted Proteomics Acquisition on a TIMS-QTOF.

Antoine Lesur1, Pierre-Olivier Schmit2, François Bernardin1

  • 1Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, L-1445 Strassen, Luxembourg.

Analytical Chemistry
|December 17, 2020
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Summary

This study introduces prm-PASEF, a novel targeted proteomics method using trapped ion mobility spectrometry (TIMS) for sensitive peptide quantification. The method achieves high reproducibility and accuracy, enabling rapid analysis of proteins like Ras in cancer cell lines.

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Biochemistry

Background:

  • Targeted proteomics enables sensitive detection of specific peptides and proteins.
  • Conventional methods face limitations in throughput and sensitivity for complex samples.

Purpose of the Study:

  • To describe a new methodology for targeted peptide quantification using a trapped ion mobility quadrupole time-of-flight mass spectrometer (timsTOF Pro).
  • To demonstrate the capability of the prm-PASEF method for sensitive and reproducible peptide quantification in complex biological matrices.

Main Methods:

  • Utilized a timsTOF Pro mass spectrometer with the prm-PASEF method.
  • Exploited trapped ion mobility spectrometry (TIMS) for precursor ion separation based on shape and charge.
  • Integrated TIMS with quadrupole time-of-flight (QTOF) mass analysis for multiplexed peptide monitoring.
  • Employed isotope-labeled synthetic peptides (AQUA peptides) for quantification.

Main Results:

  • Monitored over 200 peptides in a 30-minute liquid chromatography separation.
  • Achieved limits of quantification as low as 17.2 amol for specific peptides.
  • Demonstrated high reproducibility and accurate quantification of Ras proteins and mutations in cancer cell lines using 10-minute gradient separations.

Conclusions:

  • The prm-PASEF method significantly enhances targeted peptide quantification capabilities.
  • This approach offers high sensitivity, reproducibility, and speed for analyzing complex proteomes.
  • The methodology is suitable for accurate quantification in biological samples, including clinical applications like cancer biomarker analysis.