Bridging Simplicity and Depth in Single-Cell Proteomics: A Cost-Effective Workflow and Expanded Framework for Data Evaluation

Abstract

Single-cell proteomics (SCP) offers direct insight into functional protein states that drive cellular heterogeneity, complementing genomic and transcriptomic analyses. Although recent reports have demonstrated improved proteome coverage, their reliance on specialized instrumentation limits broader adoption. Additionally, current evaluation practices remain largely centered on protein and peptide identification counts, which alone do not fully reflect data quality or biological interpretability. Here, we describe an accessible, label-free SCP workflow which implements easily accessible laboratory equipment: a single-cell dispenser, conventional multiwell plates, and an incubator with water-bath-based humidity control. Using trapped ion mobility spectrometry-time-of-flight mass spectrometry (timsTOF), we systematically optimize key sample preparation variables, including trypsin concentration, incubation time, reduction/alkylation, digestion conditions, and plate types, which together maximize data quality and reproducibility. We further introduce a data-quality framework that moves beyond identification counts, emphasizing quantitative consistency and biological interpretability via individual protein coverage completeness across cells, coefficients of variation across technical replicates, peptide-to-protein ratios, and single-cell-to-bulk correlations. Collectively, our approach lowers technical barriers to accessing SCP while enabling more rigorous, interpretable, and scalable SCP analysis across diverse research contexts.