During
brain development, neuronal proteomes are regulated in part
by changes in spontaneous and sensory-driven activity in immature
neural circuits. A longstanding model for studying activity-dependent
circuit refinement is the developing mouse visual system where the
formation of axonal projections from the eyes to the brain is influenced
by spontaneous retinal activity prior to the onset of vision and by
visual experience after eye-opening. The precise proteomic changes
in retinorecipient targets that occur during this developmental transition
are unknown. Here, we developed a microanalytical proteomics pipeline
using capillary electrophoresis (CE) electrospray ionization (ESI)
mass spectrometry (MS) in the discovery setting to quantify developmental
changes in the chief circadian pacemaker, the suprachiasmatic nucleus
(SCN), before and after the onset of photoreceptor-dependent visual
function. Nesting CE-ESI with trapped ion mobility spectrometry time-of-flight
(TOF) mass spectrometry (TimsTOF PRO) doubled the number of identified
and quantified proteins compared to the TOF-only control on the same
analytical platform. From 10 ng of peptide input, corresponding to
<∼0.5% of the total local tissue proteome, technical triplicate
analyses identified 1894 proteins and quantified 1066 proteins, including
many with important canonical functions in axon guidance, synapse
function, glial cell maturation, and extracellular matrix refinement.
Label-free quantification revealed differential regulation for 166
proteins over development, with enrichment of axon guidance-associated
proteins prior to eye-opening and synapse-associated protein enrichment
after eye-opening. Super-resolution imaging of select proteins using
STochastic Optical Reconstruction Microscopy (STORM) corroborated
the MS results and showed that increased presynaptic protein abundance
pre/post eye-opening in the SCN reflects a developmental increase
in synapse number, but not presynaptic size or extrasynaptic protein
expression. This work marks the first development and systematic application
of TimsTOF PRO for CE-ESI-based microproteomics and the first integration
of microanalytical CE-ESI TimsTOF PRO with volumetric super-resolution
STORM imaging to expand the repertoire of technologies supporting
analytical neuroscience.