Protein Enrichment from Ascites Fluid Using Nanotrap Hydrogel Particle Technology

Ascites fluid is a clinically relevant biological matrix commonly present in patients with high-grade serous ovarian carcinoma (HGSOC). Enrichment or depletion methods are required to compress the dynamic range of the ascites fluid proteome prior to mass spectrometry (MS)-based proteomic analysis. In this study, we evaluated the ability of Nanotrap Protein Enrichment Affinity Kits (PEAK) to enable the MS detection of lower-abundance proteins in ascites fluid in a biomarker discovery workflow. Nanotrap PEAK contains magnetic hydrogel nanoparticles (A, B, and C), whose complementary chemistries selectively isolate low-abundance proteins while excluding high-abundance proteins to enhance the depth of proteome coverage. The Nanotrap particles have previously been evaluated for plasma, serum, CSF, and urine protein enrichment but not ascites fluid. The use of the Nanotrap particles resulted in >2-3× more identified proteins than the Neat ascites. An average of 61% of the proteins were enriched by the Nanotrap particles, whereas 39% were depleted. The maximum number of proteins identified among 10 HGSOC-derived ascites samples processed using the Nanotrap particles was 3480-4000 vs 1505 in the Neat samples. The use of Nanotrap particles is a cost-efficient and readily scalable approach for MS-based proteomic biomarker discovery studies in ascites fluid.