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Comprehensive Plasma N-Glycoproteome Profiling Based on EThcD-sceHCD-MS/MS.

Yonghong Mao1, Tao Su2, Tianhai Lin3

  • 1Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China.

Frontiers in Chemistry
|July 7, 2022
PubMed
Summary

We enhanced plasma N-glycoproteome analysis using EThcD-sceHCD and combinatorial peptide ligand library (CPLL) methods. This approach significantly improves the identification of intact N-glycopeptides for cancer biomarker discovery.

Keywords:
EThcD-sceHCDN-glycoproteomicscombinatorial peptide ligand librarymass spectrometryplasma

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Area of Science:

  • Biochemistry
  • Proteomics
  • Analytical Chemistry

Background:

  • Glycoproteins play crucial roles in biological processes and are key in cancer diagnostics.
  • Over one-third of FDA-approved tumor biomarkers are glycoproteins, highlighting the need for advanced characterization.
  • Systematic characterization of plasma N-glycoproteome is vital for improving diagnostic accuracy.

Purpose of the Study:

  • To compare different mass spectrometry dissociation methods for intact N-glycopeptide analysis.
  • To evaluate the integration of combinatorial peptide ligand library (CPLL) with EThcD-sceHCD for plasma N-glycoproteome profiling.
  • To assess the performance of EThcD-sceHCD, EThcD, and sceHCD in prostate cancer plasma analysis.

Main Methods:

  • Integrated combinatorial peptide ligand library (CPLL) with EThcD-sceHCD fragmentation.
  • Analyzed intact N-glycopeptides from prostate cancer plasma using EThcD-sceHCD, EThcD, and sceHCD.
  • Compared the efficiency and coverage of different mass spectrometry dissociation techniques.

Main Results:

  • EThcD-sceHCD identified twice as many intact N-glycopeptides compared to EThcD and sceHCD.
  • A combined approach using sceHCD and EThcD-sceHCD achieved 96.4% glycoprotein and 93.6% intact N-glycopeptide coverage.
  • Demonstrated good complementarity between sceHCD and EThcD-sceHCD methods.

Conclusions:

  • EThcD-sceHCD significantly enhances the identification of intact N-glycopeptides.
  • The combination of CPLL with EThcD-sceHCD and sceHCD offers comprehensive plasma N-glycoproteome profiling.
  • This integrated strategy holds promise for discovering medium- and low-abundance plasma glycoprotein biomarkers.