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Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples
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A Simple Workflow for Large Scale Shotgun Glycoproteomics.

Astrid Guldbrandsen1,2, Harald Barsnes1,3, Ann Cathrine Kroksveen1,2

  • 1Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway.

Methods in Molecular Biology (Clifton, N.J.)
|December 25, 2015
PubMed
Summary

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This study presents a new method for enriching glycosylated peptides from human cerebrospinal fluid. The approach simplifies biomarker discovery by focusing on glycosylation site identification using open-source software.

Area of Science:

  • Biochemistry
  • Proteomics
  • Analytical Chemistry

Background:

  • Glycosylation, the attachment of carbohydrates to proteins, is crucial for cellular functions.
  • Studying glycoproteins is complex due to sample heterogeneity.
  • Cerebrospinal fluid (CSF) is a valuable source for biomarker discovery.

Purpose of the Study:

  • To develop a method for enriching glycosylated peptides from human CSF.
  • To establish a data analysis pipeline for identifying site-specific glycosylation.
  • To enable more efficient biomarker studies in neurological diseases.

Main Methods:

  • Enrichment of glycosylated peptides using affinity-based methods after trypsin digestion of CSF proteins.
  • Mass spectrometry-based proteomics for peptide identification and characterization.
Keywords:
Data interpretationEnrichmentGlycoproteomics

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  • Utilizing open-source software for data analysis and glycosylation site mapping.

    • Main Results:

    • Successful enrichment of glycosylated peptides from human CSF samples.
    • Identification of site-specific glycosylation on numerous peptides.
    • Demonstration of a user-friendly workflow for analyzing complex glycopeptide data.

    Conclusions:

    • The described method effectively enriches glycosylated peptides from CSF.
    • This approach facilitates the identification of glycosylation sites, aiding biomarker discovery.
    • Open-source tools make advanced glycopeptide analysis accessible.