High-throughput Single-Cell Proteomics and Transcriptomics from the Same Cells with a Nanoliter-Scale Spin-Transfer Approach

Single-cell multiomic platforms provide a comprehensive snapshot of cellular states and cell types by offering critical insights into the spatiotemporal regulation of biomolecular networks at a systems level, thereby defining the basis of multicellularity. Here, we introduce nanoSPINS, an advanced platform that enables high-throughput profiling and integrative analysis of the transcriptome and proteome from the same single cells using RNA sequencing and isobaric labeling LC-MS-based proteomics, respectively. NanoSPINS can efficiently transfer mRNA-containing droplets between two microdevices in parallel via a spinning-based approach, while proteins are retained in the initial device. Benchmarking of nanoSPINS on two cell lines demonstrates its ability to generate global proteomic and transcriptomic profiles that align well with previously established methodologies/platforms. We demonstrated the incorporation of isobaric TMTpro labeling significantly reduces MS runtime and thereby enhances the throughput of single-cell proteomic analysis. By enabling the high-throughput quantification of the proteome and transcriptome, nanoSPINS not only facilitates the identification of putative molecular biomarkers at both mRNA and protein level but also provides larger sample sizes for improved statistical power.