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Related Concept Videos

Mass Analyzers: Common Types01:19

Mass Analyzers: Common Types

The quadrupole mass analyzer consists of four cylindrical metal rods arranged in a diamond carrying a DC voltage and a radio-frequency AC voltage. The motion of ions through the quadrupole depends on the field strength, causing only ions of a certain m/z to resonate successfully and strike the detector at a given field strength. Though the transmission rate for these analyzers is high, the exact elemental composition of the sample is not determined because of low resolution; however, they are...

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Phosphoproteomic Strategy for Profiling Osmotic Stress Signaling in Arabidopsis
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Optimized Orbitrap HCD for quantitative analysis of phosphopeptides.

Yi Zhang1, Scott B Ficarro, Shaojuan Li

  • 1Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115-6084, USA.

Journal of the American Society for Mass Spectrometry
|May 1, 2009
PubMed
Summary

This study optimizes mass spectrometry (MS) methods for improved quantitative proteomics, particularly for modified peptides. Enhanced tandem MS analysis enables accurate quantification of phosphorylated peptides and identification of signaling pathways in leukemia.

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Biochemistry

Background:

  • Radio frequency quadrupole ion traps face challenges with labile post-translational modifications in bottom-up proteomics.
  • Current MS/MS quantification methods require robust detection of low-mass fragments, which can be problematic for modified peptides.

Purpose of the Study:

  • To optimize instrument and post-acquisition parameters for enhanced quantitative proteomics.
  • To enable accurate quantification of iTRAQ-labeled phosphorylated peptides from complex biological samples.

Main Methods:

  • Utilized a multipole collision cell adjacent to an Orbitrap mass analyzer for higher-energy collisional activated dissociation (HCD).
  • Optimized collision energy as a function of precursor m/z and charge (z).
  • Applied iTRAQ (isobaric Tags for Relative and Absolute Quantitation) labeling for peptide quantification.

Main Results:

  • Achieved reliable quantification of peptides across a 100:1 concentration dynamic range.
  • Demonstrated optimal performance in peptide identification and relative quantification using iTRAQ.
  • Successfully identified activated signaling pathways downstream of oncogenic Flt-3 kinase mutants.

Conclusions:

  • Optimized HCD-Orbitrap MS/MS provides superior performance for quantitative proteomics, especially for modified peptides.
  • Parameterization of collision energy is crucial for accurate peptide identification and quantification.
  • This approach facilitates the study of signaling pathway activation in diseases like leukemia.