1DE-MS profiling of rat cerebral cortex proteins of focal cerebral ischemia-reperfusion injury by combining SDS-PAGE, gel slicing, quantitative LC-MS/MS and profile reconstruction
Description
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. All the 1DE-MS profiles were deposited in this dataset. The proteins were numbered alphabetically by their UniProtKB entry names, from #1 to #5943, as listed in "list of the 5943 proteins.xlsx". The data and the 1DE-MS profiles in two plot formats (color density and histogram) were provided in the six Excel files, each protein in a separate worksheet with the name "# protein -UniProtKB entry name" (e.g., 1536 -ALDOC_RAT). This dataset contains a significant amount of information of high complexity, which was presented visually by the 1DE-MS profiles. The observations included, 1) several hundreds of proteins were co-detected at any position in the gels, 2) about one-third of the proteins were detected at more than one positions or with broad distributions in the gels, 3) about one-fourth of the proteins were detected in the gels at the positions with the abundance-peak apparent molecular masses (Mws) obviously different from their calculated Mws, 4) the changes of a protein caused by different physiological or pathological conditions were not just about the total quantity, but of its structural information-rich profile. Examination of some 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.