DOI: 10.5061/dryad.8v2d0
title: Data from: Analysis of the cerebrospinal fluid proteome in Alzheimer's disease

description: Alzheimer’s disease is a neurodegenerative disorder accounting for more
 than 50% of cases of dementia. Diagnosis of Alzheimer’s disease relies on
 cognitive tests and analysis of amyloid beta, protein tau, and
 hyperphosphorylated tau in cerebrospinal fluid. Although these markers
 provide relatively high sensitivity and specificity for early disease
 detection, they are not suitable for monitor of disease progression. In
 the present study, we used label-free shotgun mass spectrometry to analyse
 the cerebrospinal fluid proteome of Alzheimer’s disease patients and
 non-demented controls to identify potential biomarkers for Alzheimer’s
 disease. We processed the data using five programs (DecyderMS, Maxquant,
 OpenMS, PEAKS, and Sieve) and compared their results by means of
 reproducibility and peptide identification, including three different
 normalization methods. After depletion of high abundant proteins we found
 that Alzheimer’s disease patients had lower fraction of low-abundance
 proteins in cerebrospinal fluid compared to healthy controls
 (p&lt;0.05). Consequently, global normalization was found to be less
 accurate compared to using spiked-in chicken ovalbumin for normalization.
 In addition, we determined that Sieve and OpenMS resulted in the highest
 reproducibility and PEAKS was the programs with the highest identification
 performance. Finally, we successfully verified significantly lower levels
 (p&lt;0.05) of eight proteins (A2GL, APOM, C1QB, C1QC, C1S, FBLN3,
 PTPRZ, and SEZ6) in Alzheimer’s disease compared to controls using an
 antibody-based detection method. These proteins are involved in different
 biological roles spanning from cell adhesion and migration, to regulation
 of the synapse and the immune system.
description: AD1_1Alzheimer's disease
 sample 1 technical replicate 1AD1_2Alzheimer's disease
 sample 1 technical replicate 2AD2_1Alzheimer's disease
 sample 2 technical replicate 1AD2_2Alzheimer's disease
 sample 2 technical replicate 2AD3_1Alzheimer's disease
 sample 3 technical replicate 1AD3_2Alzheimer's disease
 sample 3 technical replicate 2AD4_1Alzheimer's disease
 sample 4 technical replicate 1AD4_2Alzheimer's disease
 sample 4 technical replicate 2AD5_1Alzheimer's disease
 sample 5 technical replicate 1AD5_2Alzheimer's disease
 sample 5 technical replicate 2AD6_1Alzheimer's disease
 sample 6 technical replicate 1AD6_2Alzheimer's disease
 sample 6 technical replicate 2AD7_1Alzheimer's disease
 sample 7 technical replicate 1AD7_2Alzheimer's disease
 sample 7 technical replicate 2AD8_1Alzheimer's disease
 sample 8 technical replicate 1AD8_2Alzheimer's disease
 sample 8 technical replicate 2AD9_1Alzheimer's disease
 sample 9 technical replicate 1AD9_2Alzheimer's disease
 sample 9 technical replicate 2AD10_1Alzheimer's disease
 sample 10 technical replicate 1AD10_2Alzheimer's disease
 sample 10 technical replicate 2C1_1Healthy control sample 1
 technical replicate 1C1_2Healthy control sample 1
 technical replicate 2C2_1Healthy control sample 2
 technical replicate 1C2_2Healthy control sample 2
 technical replicate 2C3_1Healthy control sample 3
 technical replicate 1C3_2Healthy control sample 3
 technical replicate 2C4_1Healthy control sample 4
 technical replicate 1C4_2Healthy control sample 4
 technical replicate 2C5_1Healthy control sample 5
 technical replicate 1C5_2Healthy control sample 5
 technical replicate 2C6_1Healthy control sample 6
 technical replicate 1C6_2Healthy control sample 6
 technical replicate 2C7_1Healthy control sample 7
 technical replicate 1C7_2Healthy control sample 7
 technical replicate 2C8_1Healthy control sample 8
 technical replicate 1C8_2Healthy control sample 8
 technical replicate 2C9_1Healthy control sample 9
 technical replicate 1C9_2Healthy control sample 9
 technical replicate 2C10_1Healthy control sample
 10 technical replicate 1C10_2Healthy control sample
 10 technical replicate 2