Optimized proteomic analysis of a mouse model of cerebellar dysfunction using amine-specific isobaric tags

Proteomics. 2006 Aug;6(15):4321-34. doi: 10.1002/pmic.200600026.


Recent proteomic applications have demonstrated their potential for revealing the molecular mechanisms underlying neurodegeneration. The present study quantifies cerebellar protein changes in mice that are deficient in plasma membrane calcium ATPase 2 (PMCA2), an essential neuronal pump that extrudes calcium from cells and is abundantly expressed in Purkinje neurons. PMCA2-null mice display motor dyscoordination and unsteady gait deficits observed in neurological diseases such as multiple sclerosis and ataxia. We optimized an amine-specific isobaric tags (iTRAQ)-based shotgun proteomics workflow for this study. This workflow took consideration of analytical variance as a function of ion signal intensity and employed biological repeats to aid noise reduction. Even with stringent protein identification criteria, we could reliably quantify nearly 1000 proteins, including many neuronal proteins that are important for synaptic function. We identified 21 proteins that were differentially expressed in PMCA2-null mice. These proteins are involved in calcium homeostasis, cell structure and chromosome organization. Our findings shed light on the molecular changes that underlie the neurological deficits observed in PMCA2-null mice. The optimized workflow presented here will be valuable for others who plan to implement the iTRAQ method.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amines / chemistry*
  • Animals
  • Blotting, Western
  • Calbindins
  • Calcium-Transporting ATPases / deficiency
  • Calcium-Transporting ATPases / genetics
  • Calcium-Transporting ATPases / metabolism
  • Cation Transport Proteins / deficiency
  • Cation Transport Proteins / genetics
  • Cation Transport Proteins / metabolism
  • Cerebellar Diseases / genetics
  • Cerebellar Diseases / metabolism*
  • Cerebellum / metabolism
  • Cerebellum / pathology
  • Chromatography, Ion Exchange / methods
  • Computational Biology
  • Disease Models, Animal
  • Electrophoresis, Gel, Two-Dimensional
  • Mice
  • Mice, Inbred C57BL
  • Mice, Knockout
  • Plasma Membrane Calcium-Transporting ATPases
  • Proteins / analysis
  • Proteins / metabolism*
  • Proteomics / methods*
  • Reproducibility of Results
  • S100 Calcium Binding Protein G / analysis
  • S100 Calcium Binding Protein G / metabolism
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization


  • Amines
  • Calbindins
  • Cation Transport Proteins
  • Proteins
  • S100 Calcium Binding Protein G
  • Plasma Membrane Calcium-Transporting ATPases
  • Atp2b2 protein, mouse
  • Calcium-Transporting ATPases