Global mapping of rat plasma proteins with a native proteomic approach using nondenaturing micro 2DE and label-free quantitative LC-MS/MS

Plasma samples from adult male rats were separated by nondenaturing micro 2DE and a representative gel was selected, on which a total of 136 CBB-stained spots were numbered and subjected to in-gel digestion and label-free quantitative LC-MSE (MS/MS in data-independent acquisition mode). The analysis provided the assignment of 1-25 (average eight) nonredundant proteins in each spot and totally 199 proteins were assigned in the 136 spots. The quantity data from the LC-MSE analysis were further analyzed to reconstruct the quantity distribution on the 2D gel for each of the assigned proteins (a native protein map). This work provides not only a reference library containing 199 native protein maps for rat plasma proteome, but also useful information for subsequent analysis for protein-protein interactions.