Temporal Proteomic Profiling of SH-SY5Y Differentiation with Retinoic Acid Using FAIMS and Real-Time Searching

The
SH-SY5Y cell line is often used as a surrogate for neurons
in cell-based studies. This cell line is frequently differentiated
with all-trans retinoic acid (ATRA) over a 7-day
period, which confers neuron-like properties to the cells. However,
no analysis of proteome remodeling has followed the progress of this
transition. Here, we quantitatively profiled over 9400 proteins across
a 7-day treatment with retinoic acid using state-of-the-art mass spectrometry-based
proteomics technologies, including FAIMS, real-time database searching,
and TMTpro16 sample multiplexing. Gene ontology analysis revealed
that categories with the highest increases in protein abundance were
related to the plasma membrane/extracellular space. To showcase our
data set, we surveyed the protein abundance profiles linked to neurofilament
bundle assembly, neuron projections, and neuronal cell body formation.
These proteins exhibited increases in abundance level, yet we observed
multiple patterns among the queried proteins. The data presented represent
a rich resource for investigating temporal protein abundance changes
in SH-SY5Y cells differentiated with retinoic acid. Moreover, the
sample preparation and data acquisition strategies used here can be
readily applied to any analogous cell line differentiation analysis.