ABSTRACT: A rat model of focal cerebral ischemia-reperfusion (I/R) injury was established by 2 hour-middle cerebral artery occlusion (MCAO) followed with 1, 7 and 14 days of reperfusion. Validation of the model was done by the measurement on cerebral blood flow, infarct volume, histological damage and neurological functions. The rat cerebral cortex proteins from the six animal groups (sham and I/R; 1D, 7D and 14D; 4 rats per group) were analyzed with an approach we termed as "1DE-MS profiling", by combining SDS-PAGE, gel slicing, quantitative LC-MS/MS and profile reconstruction. The samples were separated by gradient SDS-PAGE and each lane of the samples was cut into a set of 35 equal-sized (1.1 mm × 1.1 mm) square pieces. All the gel pieces were analyzed with standardized procedures of in-gel digestion and LC-MS/MS. A total of 5943 proteins (37 keratins included) were detected and the MS-detected abundance data were used to reconstruct the gel distributions in the six groups for all the proteins. This dataset includes 1) all the 840 raw files (6 groups x 4 animals x 35 gel squares/sample), named as "*.raw.zip", 2) the 35 peak files, named as "*-peak list.mgf" and 35 search results, named as "*-search result.zip", from the 35 gel squares for the 24 samples, at the levels of peptide fragments, peptides and proteins, respectively, 3) the one gel pattern with the cutting and square numbering, named as "gel pattern and square numbering.pptx", 4) the one Excel file that contains all the protein-level search results and the processed results for 1DE-MS profile making, named as "Protein-level summary and processing for 1DE-MS profile plotting.xlsx", and 5) the gel distributions (termed 1DE-MS profiles) reconstructed for all the detected proteins, named "1DE-MS profiles of 5943 proteins.zip". We think this data set contains a significant amout of information on the brain proteomic changes at different time points with ischemia-reperfusion injury. The 1DE-MS profiles revealed the changes of proteins caused by different physiological or pathological conditions were not just about the total quantity, but of its structural information-rich profile. Examination of the profiles revealed the formation of the detected protein forms, often termed as "proteoforms" in recent years, involved alternative splicing, proteolytic processing, PTMs such as glycosylation, phosphorylation and ubiquitination, and degradation or fragmentation. We think this dataset would provide useful information for rat brain protein analysis and the method of 1DE-MS profiling would provide an option for proteomic analysis, from the view of proteoforms that concerns protein structures.
Ya Jin 
