Proteomic analysis of mouse astrocytes and their secretome by a combination of FASP and StageTip-based, high pH, reversed-phase fractionation

Proteomics. 2014 Jul;14(13-14):1604-9. doi: 10.1002/pmic.201300495. Epub 2014 May 28.


Astrocytes are the most abundant cells in the CNS, but their function remains largely unknown. Characterization of the whole-cell proteome and secretome in astrocytes would facilitate the study of their functions in various neurodegenerative diseases and astrocyte-neuron communication. To build a reference proteome, we established a C8-D1A astrocyte proteome to a depth of 7265 unique protein groups using a novel strategy that combined two-step digestion, filter-aided sample preparation, StageTip-based high pH fractionation, and high-resolution MS. Nearly, 6000 unique protein groups were identified from conditioned media of astrocyte cultures, constituting the largest astrocyte secretome that has been reported. High-confidence whole-cell proteomes and secretomes are valuable resources in studying astrocyte function by label-free quantitation and bioinformatics analysis. All MS data have been deposited in the ProteomeXchange with identifier PXD000501 (

Keywords: Astrocyte; High pH fractionation; LC-MS/MS; Proteome profile; Secretome; Technology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Astrocytes / chemistry*
  • Astrocytes / metabolism
  • Cell Line
  • Chromatography, Reverse-Phase / methods*
  • Hydrogen-Ion Concentration
  • Mice
  • Proteome / analysis*
  • Proteome / metabolism
  • Proteomics / methods*
  • Tandem Mass Spectrometry / methods*


  • Proteome