Data Independent Acquisition (DIA) based quantification workflow for proteome analysis of GASH/Sal and Control hamster

The GASH/Sal hamster (Genetic audiogenic seizure, Salamanca) is a model of audiogenic seizures with the epileptogenic focus localized in the inferior colliculus (IC). The sound-induced seizures exhibit a short latency (7-9 seconds), which implies innate protein disturbances in the IC as a basis for seizure susceptibility and generation. Here, we aim to study the protein profile in the GASH/Sal IC in comparison to controls. Protein samples from the IC were processed for enzymatic digestion and then analyzed by mass spectrometry in Data-Independent Acquisition mode. After identifying the proteins using the UniProt database, we selected those with differential expression. We identified 5254 proteins, of which 184 were differentially expressed, 126 upregulated and 58 downregulated. Moreover, a small number of proteins were uniquely found in the GASH/Sal or the control. The resuls indicated a protein profile alteration in the epileptogenic nucleus that might underlie the innate occuring audiogenic seizures in the GASH/Sal model.