Analysis of the rat hypothalamus proteome by data-independent label-free LC-MS/MS

Proteomics. 2012 Nov;12(22):3386-92. doi: 10.1002/pmic.201100642. Epub 2012 Oct 19.


Studies of neuronal, endocrine, and metabolic disorders would be facilitated by characterization of the hypothalamus proteome. Protein extracts prepared from 16 whole rat hypothalami were measured by data-independent label-free nano LC-MS/MS. Peptide features were detected, aligned, and searched against a rat Swiss-Prot database using ProteinLynx Global Server v.2.5. The final combined dataset comprised 21 455 peptides, corresponding to 622 unique proteins, each identified by a minimum of two distinct peptides. The majority of the proteins (69%) were cytosolic, and 16% were membrane proteins. Important proteins involved in neurological and synaptic function were identified including several members of the Ras-related protein family and proteins involved in glutamate biosynthesis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Biomarkers / analysis
  • Chromatography, Liquid / methods*
  • Databases, Protein
  • Hypothalamus / chemistry*
  • Hypothalamus / metabolism
  • Isoelectric Point
  • Nerve Tissue Proteins / analysis*
  • Nerve Tissue Proteins / chemistry
  • Peptide Fragments / analysis
  • Proteome / analysis*
  • Proteome / chemistry
  • Proteomics
  • Rats
  • Rats, Wistar
  • Tandem Mass Spectrometry / methods*


  • Biomarkers
  • Nerve Tissue Proteins
  • Peptide Fragments
  • Proteome