Enhanced Quantitative LC-MS/MS Analysis of N‑linked Glycans Derived from Glycoproteins Using Sodium Deoxycholate Detergent

Protein glycosylation is a common
protein post-translational modification
(PTM) in living organisms and has been shown to associate with multiple
diseases, and thus may potentially be a biomarker of such diseases.
Efficient protein/glycoprotein extraction is a crucial step in the
preparation of N-glycans derived from glycoproteins
prior to LC-MS analysis. Convenient, efficient and unbiased sample
preparation protocols are needed. Herein, we evaluated the use of
sodium deoxycholate (SDC) acidic labile detergent to release N-glycans of glycoproteins derived from biological samples
such as cancer cell lines. Compared to the filter-aided sample preparation
approach, the sodium deoxycholate (SDC) assisted approach was determined
to be more efficient and unbiased. SDC removal was determined to be
more efficient when using acidic precipitation rather than ethyl acetate
phase transfer. Efficient extraction of proteins/glycoproteins from
biological samples was achieved by combining SDC lysis buffer and
beads beating cell disruption. This was suggested by a significant
overall increase in the intensities of N-glycans
released from cancer cell lines. Additionally, the use of SDC approach
was also shown to be more reproducible than those methods that do
not use SDC.