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PXD008687

PXD008687 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleEnhanced Quantitative LC-MS/MS Analysis of N-linked Glycans Derived from Glycoproteins Using Sodium Deoxycholate Detergent
DescriptionProtein 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 key 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.
HostingRepositoryPRIDE
AnnounceDate2018-05-16
AnnouncementXMLSubmission_2018-05-16_02:07:36.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterWenjing Peng
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentLTQ Orbitrap Velos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02018-01-16 05:03:33ID requested
12018-05-16 02:07:37announced
Publication List
Zhu R, Zhou S, Peng W, Huang Y, Mirzaei P, Donohoo K, Mechref Y, Enhanced Quantitative LC-MS/MS Analysis of N-linked Glycans Derived from Glycoproteins Using Sodium Deoxycholate Detergent. J Proteome Res, 17(8):2668-2678(2018) [pubmed]
Keyword List
curator keyword: Technical
submitter keyword: acidic labile detergent, sodium deoxycholate, detergent removal, N-glycomics, LC-MS/MS sample preparation
Contact List
Yehia Mechref
contact affiliationDepartment of Chemistry and Biochemistry, Texas Tech University, Texas, USA
contact emailyehia.mechref@ttu.edu
lab head
Wenjing Peng
contact affiliationTexas Tech University
contact emailwenjing.peng@ttu.edu
dataset submitter
Full Dataset Link List
Dataset FTP location
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