Dataset Information

BACE1 KO mouse CSF LC-MSMS - Label-free Quantitative Proteomics of Mouse Cerebrospinal Fluid Detects β-Site APP Cleaving Enzyme (BACE1) Protease Substrates In Vivo

ABSTRACT: Analysis of murine cerebrospinal fluid (CSF) by quantitative mass spectrometry is challenging due to low CSF volume, low total protein concentration and the presence of highly abundant proteins such as albumin. We demonstrate that the CSF proteome of individual mice can be analyzed in a quantitative manner to a depth of several hundred proteins in a robust and simple workflow consisting of single ultra HPLC runs on a benchtop mass spectrometer. The workflow is validated by a comparative analysis of BACE1-/- and wild type mice using label-free quantification. The protease BACE1 cleaves the amyloid precursor protein (APP) as well as several other substrates and is a major drug target in Alzheimer’s disease. We identified a total of 715 proteins with at least 2 unique peptides and quantified 522 of those proteins in CSF from BACE1-/- and wild type mice. Several proteins, including the known BACE1 substrates APP, APLP1, CHL1 and contactin-2 showed lower abundance in the CSF of BACE1-/- mice, demonstrating that BACE1 substrate identification is possible from CSF. Additionally, ectonucleotide pyrophosphatase 5 was identified as a novel BACE1 substrate and validated by immunoblot and in vitro BACE1 protease assay. Taken together, our study shows the deepest characterization of the mouse CSF proteome to date and the first quantitative analysis of the CSF proteome of individual mice. The BACE1 substrates identified in CSF may serve as biomarkers to monitor BACE1 activity in Alzheimer patients treated with BACE inhibitors.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Cerebrospinal Fluid

SUBMITTER: Stephan Mueller

LAB HEAD: Stefan Lichtenthaler

PROVIDER: PXD001514 | Pride | 2015-10-12

REPOSITORIES: Pride

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Label-free Quantitative Proteomics of Mouse Cerebrospinal Fluid Detects β-Site APP Cleaving Enzyme (BACE1) Protease Substrates In Vivo.

Dislich Bastian B Wohlrab Felix F Bachhuber Teresa T Müller Stephan A SA Kuhn Peer-Hendrik PH Hogl Sebastian S Meyer-Luehmann Melanie M Lichtenthaler Stefan F SF

Molecular & cellular proteomics : MCP 20150702 10

Analysis of murine cerebrospinal fluid (CSF) by quantitative mass spectrometry is challenging because of low CSF volume, low total protein concentration, and the presence of highly abundant proteins such as albumin. We demonstrate that the CSF proteome of individual mice can be analyzed in a quantitative manner to a depth of several hundred proteins in a robust and simple workflow consisting of single ultra HPLC runs on a benchtop mass spectrometer. The workflow is validated by a comparative ana ...[more]

PMID: 26139848

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			Action	DRS
	APL_ALL.zip	Other
	APL_Single_Samples.zip	Other
	BACE1_KO_mouse_CSF_MQ.zip	Other
	CSF100KO_50cm_TR1.raw	Raw
	CSF100KO_50cm_TR2.raw	Raw