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Cryo-electron Microscopy01:28

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Conventional electron microscopy (EM) involves dehydration, fixation, and staining of biological samples, which distorts the native state of biological molecules and results in several artifacts. Also, the high-energy electron beam damages the sample and makes it difficult to obtain high-resolution images. These issues can be addressed using cryo-EM, which uses frozen samples and gentler electron beams. The technique was developed by Jacques Dubochet, Joachim Frank, and Richard Henderson, for...
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Updated: Jan 12, 2026

"Cell Surface Capture" Workflow for Label-Free Quantification of the Cell Surface Proteome
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Microscaled Cell Surface Proteomics for Cryo-Preserved Cells and Tissue Samples.

John R Thorup1, Sarah A Johnston2, Moe Haines1

  • 1Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

Molecular & Cellular Proteomics : MCP
|November 1, 2025
PubMed
Summary
This summary is machine-generated.

Optimized surface protein analysis methods improve diagnostics and therapeutics by enabling robust cell surface protein profiling from low-input and cryopreserved samples. These techniques enhance biomarker discovery for patient stratification.

Keywords:
N-glycoproteomecell surface proteomicsmass spectrometryproteomicssurfaceome

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Area of Science:

  • Proteomics
  • Cell Biology
  • Biomarker Discovery

Background:

  • Cell surface proteins (CSPs) are crucial for cellular functions and therapeutic targets.
  • Analyzing CSPs from limited or cryopreserved clinical samples is challenging due to technical limitations.
  • Existing proteomic workflows struggle with membrane integrity, labeling efficiency, and high background in such samples.

Purpose of the Study:

  • To optimize and compare two complementary surface enrichment strategies for low-input and cryopreserved samples.
  • To evaluate the performance of N-glycopeptide capture and wheat germ agglutinin-horseradish peroxidase proximity labeling.
  • To enable robust surfaceome characterization in translational research settings.

Main Methods:

  • Systematic comparison of oxidation-based N-glycopeptide capture and WGA-HRP proximity labeling.
  • Benchmarking across various input amounts using solid tumor (A549) and hematologic cancer (KMS-12-BM) cell lines.
  • Optimization of enzymatic dissociation protocols for tissue-derived samples (healthy endometrium).

Main Results:

  • N-glycopeptide method showed superior specificity in low-input scenarios; WGA-HRP captured complementary CSPs.
  • Over 700 CSPs identified in total, with ~175 unique identifications per method.
  • Both workflows demonstrated high reproducibility (Pearson correlation > 0.9) and detected EGFR internalization.
  • Successful CSP profiling from cryopreserved, enzymatically dissociated endometrium (<2 million cells).

Conclusions:

  • Optimized surface enrichment strategies provide robust CSP profiling from challenging clinical samples.
  • These validated workflows facilitate biomarker discovery and patient stratification in translational settings.
  • The study overcomes limitations of sample quantity and preservation for surfaceome analysis.