Rat Liver Microsomes by 2D-LC-MS/MS

Rat liver microsomes were analysed using offline strong cation exchange fractionation followed by reverse-phase chromatography coupled to quadrupole-time-of-flight high-resolution mass spectrometry using trypsin and pepsin parallel digestions. MS/MS files were searched against the UniProt protein database (release date 12-07-2011, 241 MB) by ProteinPilot software (version 4.1) using Paragon algorithm with the following parameters: Protein identification with thorough ID search effort, iodoacetamide for cysteine alkylation and no specified proteolytic enzyme, species set for rattus norvegicus with ID focus on biological modifications. Detection protein threshold of unused ProtScore > 0.05 (confidence > 10.0%) with false discovery rate (FDR) analysis. MS tolerance 0.05 Da on precursor ions and 0.1 Da on fragments. Search was performed for +2 to +4 charge states.