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Related Concept Videos

Peptide Identification Using Tandem Mass Spectrometry01:33

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Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
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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.
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Related Experiment Video

Updated: Jul 14, 2025

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Deep Proteomic Compound Profiling with the Orbitrap Ascend Tribrid Mass Spectrometer Using Tandem Mass Tags and

Steven R Shuken1, Graeme C McAlister2, William D Barshop2

  • 1Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States.

Analytical Chemistry
|October 9, 2023
PubMed
Summary

The new Orbitrap Ascend mass spectrometer enhances high-throughput proteomics by improving sensitivity and speed for accurate drug effect analysis. This advanced instrument identifies more proteins, including low-abundant ones, with greater quantitative precision.

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Drug Discovery

Background:

  • Tandem mass tags (TMT) and tribrid mass spectrometers are vital for high-throughput proteomics.
  • Current limitations in sensitivity and speed hinder deep proteomic profiling for drug studies.
  • The Orbitrap Ascend mass spectrometer was developed to overcome these challenges.

Purpose of the Study:

  • To evaluate the performance of the new Orbitrap Ascend mass spectrometer for deep proteomic profiling.
  • To assess its capabilities in quantifying drug-induced proteome changes with high accuracy and speed.
  • To compare its performance against the existing Orbitrap Eclipse system.

Main Methods:

  • Utilized the Orbitrap Ascend mass spectrometer for proteomic analysis.
  • Employed Tandem Mass Tags (TMT) for quantitative measurements.
  • Analyzed fractionated samples and drug-treated cancer cells (HCT116) with PIN1 inhibitors.

Main Results:

  • The Ascend demonstrated increased sensitivity and higher signal-to-noise ratios compared to the Eclipse, especially with short injection times.
  • Identified and quantified significantly more peptides and proteins, including low-abundant ones, with improved quantitative precision.
  • Quantified over 8000 proteins in less instrument time and detected therapeutically relevant protein changes missed by the Eclipse.

Conclusions:

  • The Orbitrap Ascend significantly advances high-throughput proteomics, offering enhanced sensitivity, speed, and quantitative accuracy.
  • It enables deeper proteomic profiling and more precise characterization of drug effects, particularly for low-abundant proteins.
  • This technology facilitates a better understanding of drug-target interactions and structure-activity relationships, aiding in cancer drug development.