High-capacity peptide-centric platform to decode the proteomic response to brain injury

Traumatic brain injury (TBI) is a progressive disease process underlain by dynamic and interactive biochemical mechanisms; thus, large-scale and unbiased assessments are needed to fully understand its highly complex pathobiology. Here, we report on a new high-capacity label-free proteomic platform to evaluate the post-TBI neuroproteome. Six orthogonal separation stages and data-independent MS were employed, affording reproducible quantitative assessment on 18 651 peptides across biological replicates. From these data 3587 peptides were statistically responsive to TBI of which 18% were post-translationally modified. Results revealed as many as 484 proteins in the post-TBI neuroproteome, which was fully nine times the number determined from our prior study of focal cortical injury. Yet, these data were generated using 25 times less brain tissue per animal relative to former methodology, permitting greater anatomical specificity and proper biological replication for increased statistical power. Exemplified by these data, we discuss benefits of peptide-centric differential analysis to more accurately infer novel biological findings testable in future hypothesis-driven research. The high-capacity label-free proteomic platform is designed for multi-factor studies aimed at expanding our knowledge on the molecular underpinnings of TBI and to develop better diagnostics and therapeutics.