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Studying Mitochondrial Structure and Function in Drosophila Ovaries
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Targeted Proteomics to Study Mitochondrial Biology.

Justina C Wolters1,2,3, Hjalmar P Permentier1, Barbara M Bakker2,3

  • 1Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands.

Advances in Experimental Medicine and Biology
|August 28, 2019
PubMed
Summary
This summary is machine-generated.

This chapter details setting up targeted mass spectrometry assays for protein quantification using selected reaction monitoring (SRM). It provides a guide for designing and developing SRM assays for mitochondrial proteins, exemplified by succinate dehydrogenase.

Keywords:
Mass spectrometryMitochondriaProtein quantificationTargeted proteomics

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Area of Science:

  • Proteomics
  • Biochemistry
  • Analytical Chemistry

Background:

  • Targeted mass spectrometry using selected reaction monitoring (SRM) or parallel reaction monitoring (PRM) is crucial for quantifying proteins via signature peptides.
  • SRM enables simultaneous quantification of multiple proteins, such as enzymes in a biochemical pathway.

Purpose of the Study:

  • To provide a detailed guide on establishing an SRM assay for protein quantification.
  • To illustrate the process using the mitochondrial protein succinate dehydrogenase [ubiquinone] flavoprotein subunit (mouse UniProt-code Q8K2B3) as an example.

Main Methods:

  • In silico assay design, including peptide selection based on various properties.
  • LC-MS assay development, focusing on optimal peptide charge state and fragment ion selection.
  • Discussion of dynamic range for sensitive protein detection.

Main Results:

  • The chapter outlines a systematic approach to SRM assay development for targeted proteomics.
  • It demonstrates the application of these methods in quantifying mitochondrial proteins from mouse liver mitochondria.

Conclusions:

  • Effective SRM assay design and development are essential for accurate protein quantification in complex biological samples.
  • This methodology is applicable to studies investigating biological processes like mitochondrial function and aging.