Superparamagnetic Composite Nanobeads Anchored with Molecular Glues for Ultrasensitive Label-free Proteomics

Mass spectrometry has emerged as a mainstream technique for label-free proteomics. However, proteomic coverage for trace samples is constrained by adsorption loss during repeated elution at sample pretreatment. Here, we demonstrated superparamagnetic composite nanoparticles functionalized with molecular glues (MGs) to enrich proteins in trace human biofluid. We showed high protein binding (> 95%) and recovery (. 90%) rates by anchor-nanoparticles. We further proposed a Streamlined Workflow based on Anchor-nanoparticles for Proteomics (SWAP) method that enabled unbiased protein capture, protein digestion and pure peptides elution in one single tube. We demonstrated SWAP to quantify over 2500 protein groups with 100 HEK 293T cells. We adopted SWAP to profile proteomics with trace aqueous humor samples from cataract (n= 15) and wet age-related macular degeneration (n= 8) patients, and quantified approximate to 1400 proteins from 5 mu L aqueous humor. SWAP simplifies sample preparation steps, minimizes adsorption loss and improves protein coverage for label-free proteomics with previous trace samples.

Automated summary

Mass spectrometry has become a mainstream technique for label-free proteomics, but the proteomic coverage for trace samples is limited by adsorption loss during repeated elution. In this study, superparamagnetic composite nanoparticles functionalized with molecular glues were used to enrich proteins in trace human biofluid, and a streamlined workflow method was proposed to achieve unbiased protein capture, digestion, and elution. This method greatly simplified sample preparation steps, minimized adsorption loss, and improved protein coverage for label-free proteomics with trace samples.