Measurements of heterogeneity in proteomics analysis of the nanoparticle protein corona across core facilities

Abstract

Robust characterization of the protein corona—the layer of proteins that spontaneously forms on the surface of nanoparticles immersed in biological fluids—is vital for prediction of the safety, biodistribution, and diagnostic/therapeutic efficacy of nanomedicines. Protein corona identity and abundance characterization is entirely dependent on liquid chromatography coupled to mass spectroscopy (LC-MS/MS), though the variability of this technique for the purpose of protein corona characterization remains poorly understood. Here we investigate the variability of LC-MS/MS workflows in analysis of identical aliquots of protein coronas by sending them to different proteomics core-facilities and analyzing the retrieved datasets. While the shared data between the cores correlate well, there is considerable heterogeneity in the data retrieved from different cores. Specifically, out of 4022 identified unique proteins, only 73 (1.8%) are shared across the core facilities providing semiquantitative analysis. These findings suggest that protein corona datasets cannot be easily compared across independent studies and more broadly compromise the interpretation of protein corona research, with implications in biomarker discovery as well as the safety and efficacy of our nanoscale biotechnologies.

The Potential of ICP-MS as a Complementary Tool in Nanoparticle–Protein Corona Analysis

“…The formation of the protein corona creates a different structure that will drive and influence the behavior and interaction of the nanoparticles with biological systems. Thus, the protein corona can alter the interactions of the nanoparticle with the cell surface moieties (e.g., antibodies), promoting or inhibiting the uptake of the nanoparticle by the cell [ 18 ]. For instance, in a case of study with silica nanoparticle, it was observed that the formation of the protein corona reduced the cell uptake by weakening their cell membrane adhesion [ 19 ].…”

“…This final location will then determine the effect of the NPPC and the pathways or processes it gets involved in, disrupts, or promotes. Likewise, it can be used as a vehicle for drug delivery [ 18 ], or for the promoted accumulation of nanoparticles in specific areas, e.g., tumors, and serve as a biomarker or therapeutical target [ 9 ]. Naturally, the presence of nanoparticles in biological systems and their use in biomedicine brings a potential safety and toxicological risk.…”

The Issue of Reliability and Repeatability of Analytical Measurement in Industrial and Academic Nanomedicine

“…21 More specifically, by sending identical nanoparticle protein corona to 17 different mass spectroscopy centers for an analysis of the results, only 1.8% of identified unique proteins were shared across the centers. 21 The outcomes of this study suggest the urgent need for development of new standard protocols for protein corona analysis.…”

“…Academia can also find the need for development of new standards that can have a profound role in improving the safety and diagnostic/therapeutic efficacy of nanomedicine technologies. For example, very recent finding on evaluation of protein coronathe layer of proteins that forms on the surface of nanomedicines upon their interactions with biological fluidsrevealed that mass spectroscopy variations (in protocols and instruments) can cause unexpected variations in the outcomes of protein corona . More specifically, by sending identical nanoparticle protein corona to 17 different mass spectroscopy centers for an analysis of the results, only 1.8% of identified unique proteins were shared across the centers .…”

“…For example, very recent finding on evaluation of protein corona�the layer of proteins that forms on the surface of nanomedicines upon their interactions with biological fluids� revealed that mass spectroscopy variations (in protocols and instruments) can cause unexpected variations in the outcomes of protein corona. 21 More specifically, by sending identical nanoparticle protein corona to 17 different mass spectroscopy centers for an analysis of the results, only 1.8% of identified unique proteins were shared across the centers. 21 The outcomes of this study suggest the urgent need for development of new standard protocols for protein corona analysis.…”