Data from: Analysis of the cerebrospinal fluid proteome in Alzheimer's disease

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<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<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.