Protein Enrichment from Ascites Fluid Using Nanotrap Hydrogel Particle Technology

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Publication: Twigg et al., Journal of Proteome Research (2026)

Overview

This study evaluated the performance of Nanotrap® Protein Enrichment Affinity Kits (PEAK) for mass spectrometry-based proteomic analysis of ascites fluid from patients with high-grade serous ovarian cancer (HGSOC). Because ascites contains abundant plasma proteins that mask low-abundance biomarkers, the authors investigated whether Nanotrap hydrogel particles could improve proteome coverage by selectively enriching low-abundance proteins while excluding high-abundance species.

Key Findings

Significantly improved proteome depth

• Nanotrap enrichment identified more than 2–3× as many proteins as direct (neat) ascites analysis.

• Across 10 clinical ascites samples, Nanotrap-enriched workflows identified 3,480–4,000 proteins, compared with 1,505 proteins in unenriched samples.

Effective dynamic range compression

• Albumin, which represented 74% of the neat ascites proteome, was reduced to approximately 1.5% following enrichment.

• The remaining (lower-abundance) proteome was enriched 4.8–7.1-fold, substantially improving detection of potential biomarker candidates.

Complementary particle chemistries

• Three Nanotrap particle types (A, B, and C) exhibited distinct capture profiles due to differences in affinity chemistry and surface charge.

• Multi-particle combinations generally identified more proteins than individual particle types, demonstrating complementary enrichment capabilities.

Selective enrichment rather than simple depletion

• On average, 61% of quantified proteins were enriched, while 39% were depleted, indicating that Nanotrap particles selectively reshape the detectable proteome through affinity capture and molecular sieving rather than acting solely as an abundant protein depletion method.

Reproducible performance

• Technical reproducibility remained strong across enrichment methods, with median coefficients of variation between 10–22%.

• The AC and ABC particle combinations demonstrated the best balance of proteome coverage and reproducibility for biomarker discovery applications.

  
  

Implications for Nanotrap Technology

This study demonstrates that Nanotrap PEAK substantially enhances proteomic analysis of ascites fluid by:

• Increasing protein identifications and proteome depth.

• Removing interference from highly abundant plasma proteins.

• Enabling detection of lower-abundance proteins that may serve as predictive or prognostic biomarkers.

• Providing a scalable, magnetic, and automation-compatible sample preparation workflow suitable for mass spectrometry-based biomarker discovery.

Conclusion

The authors conclude that Nanotrap PEAK is a cost-effective, scalable, and reproducible enrichment technology that significantly improves the analytical performance of LC-MS/MS for complex biofluids such as ascites. By compressing the dynamic range and expanding detectable proteome coverage, Nanotrap particles provide a powerful sample preparation approach for ovarian cancer biomarker discovery and other clinical proteomics applications.

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