An optimized quantitative proteomics method establishes the cell type-resolved mouse brain secretome

EMBO J. 2020 Oct 15;39(20):e105693. doi: 10.15252/embj.2020105693. Epub 2020 Sep 21.


To understand how cells communicate in the nervous system, it is essential to define their secretome, which is challenging for primary cells because of large cell numbers being required. Here, we miniaturized secretome analysis by developing the "high-performance secretome protein enrichment with click sugars" (hiSPECS) method. To demonstrate its broad utility, hiSPECS was used to identify the secretory response of brain slices upon LPS-induced neuroinflammation and to establish the cell type-resolved mouse brain secretome resource using primary astrocytes, microglia, neurons, and oligodendrocytes. This resource allowed mapping the cellular origin of CSF proteins and revealed that an unexpectedly high number of secreted proteins in vitro and in vivo are proteolytically cleaved membrane protein ectodomains. Two examples are neuronally secreted ADAM22 and CD200, which we identified as substrates of the Alzheimer-linked protease BACE1. hiSPECS and the brain secretome resource can be widely exploited to systematically study protein secretion and brain function and to identify cell type-specific biomarkers for CNS diseases.

Keywords: CSF; BACE1; brain cells; proteomics; secretomics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • ADAM Proteins / cerebrospinal fluid
  • ADAM Proteins / metabolism
  • Amyloid Precursor Protein Secretases / antagonists & inhibitors
  • Amyloid Precursor Protein Secretases / cerebrospinal fluid
  • Amyloid Precursor Protein Secretases / metabolism*
  • Animals
  • Antigens, CD / cerebrospinal fluid
  • Antigens, CD / metabolism
  • Aspartic Acid Endopeptidases / antagonists & inhibitors
  • Aspartic Acid Endopeptidases / cerebrospinal fluid
  • Aspartic Acid Endopeptidases / metabolism*
  • Astrocytes / metabolism*
  • Brain / cytology
  • Brain / metabolism*
  • Cells, Cultured
  • Cerebrospinal Fluid Proteins
  • Chromatography, Liquid
  • Gene Ontology
  • Lipopolysaccharides / pharmacology
  • Mice
  • Mice, Inbred C57BL
  • Microglia / metabolism*
  • Nerve Tissue Proteins / cerebrospinal fluid
  • Nerve Tissue Proteins / metabolism
  • Neurons / metabolism*
  • Oligodendroglia / metabolism*
  • Principal Component Analysis
  • Proteome / metabolism
  • Proteomics / methods*
  • Software*
  • Tandem Mass Spectrometry


  • Antigens, CD
  • Cerebrospinal Fluid Proteins
  • Lipopolysaccharides
  • Nerve Tissue Proteins
  • Proteome
  • Amyloid Precursor Protein Secretases
  • Aspartic Acid Endopeptidases
  • Bace1 protein, mouse
  • ADAM Proteins
  • Adam22 protein, mouse
  • antigens, CD200