Proteome Profiling of Rat Brain Cortical Changes during Early Postnatal Brain Development

Label-free
quantitation (LFQ) was applied to proteome profiling
of rat brain cortical development during the early postnatal period.
Male and female rat brain extracts were prepared using a convenient,
detergent-free sample preparation technique at postnatal days (PND)
2, 8, 15, and 22. The PND protein ratios were calculated using Proteome
Discoverer, and the PND protein change profiles were constructed separately
for male and female animals for key presynaptic, postsynaptic, and
adhesion brain proteins. The profiles were compared to the analogous
profiles assembled from the published mouse and rat cortex proteomic
data, including the fractionated-synaptosome data. The PND protein-change
trendlines, Pearson correlation coefficient (PCC), and linear regression
analysis of the statistically significant PND protein changes were
used in the comparative analysis of the datasets. The analysis identified
similarities and differences between the datasets. Importantly, there
were significant similarities in the comparison of the rat cortex
PND (current work) vs mouse (previously published) PND profiles, although
in general, a lower abundance of synaptic proteins in mice than in
rats was found. The male and female rat cortex PND profiles were expectedly
almost identical (98–99% correlation by PCC), which also substantiated
this LFQ nanoflow liquid chromatography–high-resolution mass
spectrometry approach.