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Optimization of Mass Spectrometry-Compatible Surfactants for Shotgun Proteomics

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Department of Cell Biology, 10550 North Torrey Pines Road, SR11, The Scripps Research Institute, La Jolla, California 92037, and Protein Discovery, Inc., Knoxville, Tennessee 37902
Cite this: J. Proteome Res. 2007, 6, 7, 2529–2538
Publication Date (Web):May 27, 2007
https://doi.org/10.1021/pr060682a
Copyright © 2007 American Chemical Society
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    Abstract

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    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 5 μg 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.

    Keywords: shotgun proteomics • mass spectrometry • proteolysis • cancer cells • protein profiling

    †

     The Scripps Research Institute.

    ‡

     Protein Discovery, Inc.

    *

     To whom correspondence should be addressed: John R. Yates, III, The Scripps Research Institute, 10550 North Torrey Pines Road, SR 11, La Jolla, CA 92037. E-mail, [email protected]; phone, (858) 784-8862; fax, (858) 784-8883.

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