Optimization of mass spectrometry-compatible surfactants for shotgun proteomics

J Proteome Res. 2007 Jul;6(7):2529-38. doi: 10.1021/pr060682a. Epub 2007 May 27.


An optimization and comparison of trypsin digestion strategies for peptide/protein identifications by microLC-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 5 microg 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-abundance proteins.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Cell Extracts / chemistry
  • Mass Spectrometry*
  • Mice
  • Pancreas / chemistry
  • Pancreas / cytology
  • Peptides / analysis*
  • Peptides / chemistry
  • Proteomics / methods*
  • Solubility
  • Solutions
  • Solvents / chemistry
  • Surface-Active Agents / chemistry*
  • Trypsin / chemistry*


  • Cell Extracts
  • Peptides
  • Solutions
  • Solvents
  • Surface-Active Agents
  • Trypsin