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Simultaneous analysis of phosphorylation and glycosylation is now possible using an optimized enrichment workflow. This method enhances understanding of these crucial protein modifications in biological processes and diseases.

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Area of Science:

  • Proteomics
  • Biochemistry
  • Molecular Biology

Background:

  • Modified peptides, such as phosphopeptides and intact glycopeptides (IGPs), are crucial for studying cellular functions but are low in abundance.
  • Existing enrichment methods for phosphopeptides and IGPs are robust but often lead to coenrichment.

Purpose of the Study:

  • To develop an optimized workflow for the simultaneous enrichment and analysis of phosphopeptides and IGPs.
  • To investigate the optimal conditions for IMAC-based enrichment of phosphopeptides while minimizing IGP coenrichment.

Main Methods:

  • Immobilized metal affinity chromatography (IMAC) enrichment was performed at various pH conditions to optimize phosphopeptide isolation.
  • Hydrophilic enrichment strategies were evaluated before and after IMAC to determine the best workflow for simultaneous analysis.
  • The optimized workflow was applied to TMT-labeled peptides from breast cancer patient-derived xenograft (PDX) models.

Main Results:

  • Enrichment of phosphopeptides at pH 2.0 yielded the highest number of phosphopeptide identifications, though coenrichment with IGPs was unavoidable.
  • A workflow involving IMAC enrichment followed by hydrophilic enrichment was selected as optimal for simultaneous phospho- and glycoproteomics.
  • Quantitative analysis identified 17582 phosphopeptides and 3468 glycopeptides, with 1237 phosphopeptides and 236 glycopeptides showing significant expression differences between breast cancer subtypes.

Conclusions:

  • The developed method enables simultaneous quantitative analysis of both phosphorylation and glycosylation.
  • This advancement extends the understanding of the roles of glycosylation and phosphorylation in biological systems and disease states.