Optimization of Mass Spectrometry Compatible Surfactants for Shotgun Proteomics

摘要

An optimization and comparison of trypsin digestion strategies for peptide/protein identifications by μLC-MS/MS with or without MS compatible detergents in mixed organic-aqueous and aqueous systems was carried out in this study. We determine that adding MS compatible detergents to proteolytic digestion protocols dramatically increases peptide and protein identifications in complex protein mixtures by shotgun proteomics. Protein solubilization and proteolytic efficiency are increased by including MS compatible detergents in trypsin digestion buffers. A modified trypsin digestion protocol incorporating the MS compatible detergents consistently identifies over 300 proteins from 5ug of pancreatic cell lysates and generates a greater number of peptide identifications than trypsin digestion with urea when using LC/MS/MS. Furthermore, over 700 proteins were identified by merging protein identifications from trypsin digestion with three different MS compatible detergents. We also observe that the use of mixed aqueous and organic solvent systems can influence protein identifications in combinations with different MS compatible detergents. Peptide mixtures generated from different MS compatible detergents and buffer combinations show a significant difference in hydrophobicity. Our results show that protein digestion schemes incorporating MS compatible detergents generate quantitative as well as qualitative changes in observed peptide identifications, which lead to increased protein identifications overall and potentially increased identification of low abundant proteins.