Protein Aggregation Capture on Microparticles Enables Multipurpose Proteomics Sample Preparation*

The phenomenon of protein aggregation capture (PAC) on a wide range of different microparticles is described. Exploiting this mechanism enables generation of clean peptide mixtures from cell lines, tissues, and protein pulldowns for proteomics, phosphoproteomics, and secretomics analysis. The findings vastly increase the accessibility of the method that may ultimately lead to low cost and automated proteomics workflows. Graphical Abstract Highlights Insoluble protein aggregates preferentially precipitate on microparticles. The protein aggregation capture (PAC) occurs irrespective of microparticle surface chemistry. This process can be exploited for multi-purpose proteomics sample preparation. Facilitates potential for low cost, efficient and high-sensitivity proteomics workflows. Universal proteomics sample preparation is challenging because of the high heterogeneity of biological samples. Here we describe a novel mechanism that exploits the inherent instability of denatured proteins for nonspecific immobilization on microparticles by protein aggregation capture. To demonstrate the general applicability of this mechanism, we analyzed phosphoproteomes, tissue proteomes, and interaction proteomes as well as dilute secretomes. The findings present a practical, sensitive and cost-effective proteomics sample preparation method.