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Related Experiment Video

Updated: Dec 23, 2025

A Simple Fractionated Extraction Method for the Comprehensive Analysis of Metabolites, Lipids, and Proteins from a Single Sample
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A Simple Fractionated Extraction Method for the Comprehensive Analysis of Metabolites, Lipids, and Proteins from a Single Sample

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Serial in-solution digestion protocol for mass spectrometry-based glycomics and proteomics analysis.

Manveen K Sethi1, Margaret Downs, Joseph Zaia

  • 1Boston University School of Medicine, Boston University, Department of Biochemistry, Boston, 02118, USA. jzaia@bu.edu.

Molecular Omics
|April 21, 2020
PubMed
Summary

This study presents a new, efficient mass spectrometry method for analyzing both glycans and proteins in a single sample. This combined glycomics and proteomics approach enhances the study of complex biological processes and diseases.

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Related Experiment Videos

Last Updated: Dec 23, 2025

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Area of Science:

  • Biochemistry
  • Neuroscience
  • Analytical Chemistry

Background:

  • Mass spectrometry has advanced proteomics, but analyzing protein post-translational modifications (PTMs), especially glycosylation, remains challenging.
  • Glycosylation is a common PTM vital for biological processes, and its analysis alongside proteins is crucial for understanding complex biological systems.
  • The brain extracellular matrix (ECM), rich in glycosylated proteins like proteoglycans (PGs), is critical in neuroscience and implicated in neuropsychiatric diseases.

Purpose of the Study:

  • To develop a high-throughput method integrating glycomics and proteomics for comprehensive analysis of biomolecules.
  • To establish an efficient and economical protocol for simultaneous isolation and analysis of glycosaminoglycans (GAGs) and peptides from biological samples.
  • To improve protein identification by facilitating peptide analysis through GAG removal.

Main Methods:

  • Integration of glycomics and proteomics using a filter-aided sample preparation (FASP) based serial in-solution digestion.
  • Simultaneous isolation and analysis of multiple GAG classes (hyaluronan, chondroitin sulfate, heparan sulfate) and peptides.
  • Analysis of cleaned GAGs and peptides using liquid chromatography-tandem mass spectrometry (LC-MS/MS).

Main Results:

  • Demonstration of a single-pot protocol for processing tissue or cell lysates, more efficient than parallel methods.
  • Improved protein identification with higher peptide coverage due to the removal of interfering GAGs.
  • Successful high-throughput mass spectrometry-based glycomic and proteomic analysis, with data available via ProteomeXchange (PXD017513).

Conclusions:

  • The developed protocol offers an efficient and economical approach for combined glycomic and proteomic analysis.
  • This method facilitates a more complete biological picture by simultaneously analyzing GAGs and proteins.
  • The protocol is valuable for studying complex biological systems, particularly the brain ECM and its role in disease.