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Title: Simple Sodium Dodecyl Sulfate-Assisted Sample Preparation Method for LC-MS-based Proteomic Applications

Abstract

Sodium dodecyl sulfate (SDS) is one of the most popular laboratory reagents used for highly efficient biological sample extraction; however, SDS presents a significant challenge to LC-MS-based proteomic analyses due to its severe interference with reversed-phase LC separations and electrospray ionization interfaces. This study reports a simple SDS-assisted proteomic sample preparation method facilitated by a novel peptide-level SDS removal protocol. After SDS-assisted protein extraction and digestion, SDS was effectively (>99.9%) removed from peptides through ion substitution-mediated DS- precipitation with potassium chloride (KCl) followed by {approx}10 min centrifugation. Excellent peptide recovery (>95%) was observed for less than 20 {mu}g of peptides. Further experiments demonstrated the compatibility of this protocol with LC-MS/MS analyses. The resulting proteome coverage from this SDS-assisted protocol was comparable to or better than those obtained from other standard proteomic preparation methods in both mammalian tissues and bacterial samples. These results suggest that this SDS-assisted protocol is a practical, simple, and broadly applicable proteomic sample processing method, which can be particularly useful when dealing with samples difficult to solubilize by other methods.

Authors:
; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
1038644
Report Number(s):
PNNL-SA-84751
36197; 400412000; TRN: US201208%%736
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Analytical Chemistry; Journal Volume: 84; Journal Issue: 6
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; CENTRIFUGATION; COMPATIBILITY; DIGESTION; IONIZATION; PEPTIDES; POTASSIUM CHLORIDES; PRECIPITATION; PROCESSING; PROTEINS; REMOVAL; SAMPLE PREPARATION; SODIUM; SULFATES; SDS removal; proteomics; sample preparation; LC-MS; MASS-SPECTROMETRY; PROTEIN IDENTIFICATIONS; SDS; LECTROPHORESIS; SURFACTANTS; DETERGENTS; SEQUENCES; Environmental Molecular Sciences Laboratory

Citation Formats

Zhou, Jianying, Dann, Geoffrey P., Shi, Tujin, Wang, Lu, Gao, Xiaoli, Su, Dian, Nicora, Carrie D., Shukla, Anil K., Moore, Ronald J., Liu, Tao, Camp, David G., Smith, Richard D., and Qian, Weijun. Simple Sodium Dodecyl Sulfate-Assisted Sample Preparation Method for LC-MS-based Proteomic Applications. United States: N. p., 2012. Web. doi:10.1021/ac203394r.
Zhou, Jianying, Dann, Geoffrey P., Shi, Tujin, Wang, Lu, Gao, Xiaoli, Su, Dian, Nicora, Carrie D., Shukla, Anil K., Moore, Ronald J., Liu, Tao, Camp, David G., Smith, Richard D., & Qian, Weijun. Simple Sodium Dodecyl Sulfate-Assisted Sample Preparation Method for LC-MS-based Proteomic Applications. United States. doi:10.1021/ac203394r.
Zhou, Jianying, Dann, Geoffrey P., Shi, Tujin, Wang, Lu, Gao, Xiaoli, Su, Dian, Nicora, Carrie D., Shukla, Anil K., Moore, Ronald J., Liu, Tao, Camp, David G., Smith, Richard D., and Qian, Weijun. Sat . "Simple Sodium Dodecyl Sulfate-Assisted Sample Preparation Method for LC-MS-based Proteomic Applications". United States. doi:10.1021/ac203394r.
@article{osti_1038644,
title = {Simple Sodium Dodecyl Sulfate-Assisted Sample Preparation Method for LC-MS-based Proteomic Applications},
author = {Zhou, Jianying and Dann, Geoffrey P. and Shi, Tujin and Wang, Lu and Gao, Xiaoli and Su, Dian and Nicora, Carrie D. and Shukla, Anil K. and Moore, Ronald J. and Liu, Tao and Camp, David G. and Smith, Richard D. and Qian, Weijun},
abstractNote = {Sodium dodecyl sulfate (SDS) is one of the most popular laboratory reagents used for highly efficient biological sample extraction; however, SDS presents a significant challenge to LC-MS-based proteomic analyses due to its severe interference with reversed-phase LC separations and electrospray ionization interfaces. This study reports a simple SDS-assisted proteomic sample preparation method facilitated by a novel peptide-level SDS removal protocol. After SDS-assisted protein extraction and digestion, SDS was effectively (>99.9%) removed from peptides through ion substitution-mediated DS- precipitation with potassium chloride (KCl) followed by {approx}10 min centrifugation. Excellent peptide recovery (>95%) was observed for less than 20 {mu}g of peptides. Further experiments demonstrated the compatibility of this protocol with LC-MS/MS analyses. The resulting proteome coverage from this SDS-assisted protocol was comparable to or better than those obtained from other standard proteomic preparation methods in both mammalian tissues and bacterial samples. These results suggest that this SDS-assisted protocol is a practical, simple, and broadly applicable proteomic sample processing method, which can be particularly useful when dealing with samples difficult to solubilize by other methods.},
doi = {10.1021/ac203394r},
journal = {Analytical Chemistry},
number = 6,
volume = 84,
place = {United States},
year = {Sat Mar 10 00:00:00 EST 2012},
month = {Sat Mar 10 00:00:00 EST 2012}
}