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PXD008687

DataSet Summary

  • HostingRepository: PRIDE
  • AnnounceDate: 2018-05-16
  • AnnouncementXML: Submission_2018-05-16_02:07:36.xml
  • DigitalObjectIdentifier:
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original data
  • RepositorySupport: Unsupported dataset by repository
  • PrimarySubmitter: Wenjing Peng
  • Title: Enhanced Quantitative LC-MS/MS Analysis of N-linked Glycans Derived from Glycoproteins Using Sodium Deoxycholate Detergent
  • Description: 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 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.
  • SpeciesList: scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
  • ModificationList: monohydroxylated residue; iodoacetamide derivatized residue
  • Instrument: LTQ Orbitrap Velos

Dataset History

VersionDatetimeStatusChangeLog Entry
02018-01-16 05:03:33ID requested
12018-05-16 02:07:37announced

Publication List

  1. 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

  1. curator keyword: Technical
  2. submitter keyword: acidic labile detergent, sodium deoxycholate, detergent removal, N-glycomics, LC-MS/MS sample preparation

Contact List

    Yehia Mechref
    • contact affiliation: Department of Chemistry and Biochemistry, Texas Tech University, Texas, USA
    • contact email: yehia.mechref@ttu.edu
    • lab head:
    Wenjing Peng
    • contact affiliation: Texas Tech University
    • contact email: wenjing.peng@ttu.edu
    • dataset submitter:

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