SingPro 2.0: a proteomics-centric knowledge base for single-cell multimodal profiling.

Protein-inclusive single-cell multimodal profiling has emerged as a transformative strategy for resolving cellular heterogeneity by jointly measuring proteins and complementary molecular features in the same cells. The resulting protein-inclusive datasets are increasingly used to characterize cellular states, construct multimodal cell atlases, and decode disease mechanisms. However, such data are rarely included in existing databases. In this study, SingPro was updated from a single-cell proteomics database into a proteomics-centric knowledge base for single-cell multimodal profiling. Distinct from existing resources, the updated SingPro (a) systematically curates data and experimental details from 814 protein-inclusive multimodal studies encompassing ~81.5 million cells across 29 tissues, 44 diseases, and multiple species; (b) covers 5 omics modalities through 12 experimental technologies that simultaneously profile proteins with messenger RNA, chromatin accessibility, or other measurements in the same cell; and (c) provides cross-modality visualization for joint analysis. SingPro is freely accessible without requiring login or registration at: https://idrblab.org/singpro/.