Journal
JOURNAL OF PROTEOME RESEARCH
Volume 9, Issue 6, Pages 2863-2870Publisher
AMER CHEMICAL SOC
DOI: 10.1021/pr900949p
Keywords
Sodium Dodecyl Sulfate; SDS; SDS-PAGE; GeLC; GELFrEE; Mass Spectrometry; Proteins; Suppression; Bottom-Up; Top-Down
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Funding
- Natural Sciences and Engineering Research Council of Canada
- Canada Foundation for Innovation
- Nova Scotia Research and Innovation Trust
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SDS has recognized benefits for protein sample preparation, including solubilization and imparting molecular weight separation (e.g., SDS-PAGE). Here, we compare two proteome workflows which incorporate SDS for protein separation, namely, SDS-PAGE coupled to LC/MS (GeLC MS), along with a solution separation platform, GELFrEE, for intact proteome prefractionation and identification. Despite the clear importance of SDS in these and other proteome analysis workflows, the affect of SDS on an LC/MS proteome experiment has not been quantified. We first examined the influence of SDS on both a bottom-up as well as a top-down (intact protein) MS workflow. Surprisingly, at levels up to 0.01% SDS in the injected sample, reliable MS characterization is obtained. We subsequently explored organic precipitation protocols (chloroform/methanol/water and acetone) as a means of lowering SDS, and present a simple modified acetone precipitation protocol which consistently enables MS proteome characterizations from samples initially containing 2% SDS. With this effective strategy for SDS reduction, the GELFrEE MS workflow for bottom-up proteome analysis was characterized relative to GeLC MS. Remarkable agreement in the number and type of identified proteins was obtained from these two separation platforms, validating the use of SDS in solution-phase proteome analysis.
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