π-SeqOmics: A Sequential Workflow for Genomic, Transcriptomic, Proteomic and Phosphoproteomic Profiling from Biopsy-Scale Samples

Abstract Comprehensive multi-omics profiling from a single limited specimen remains challenging, as current extraction methods are difficult to standardize and often compromise balanced recovery of nucleic acids and proteins. Here, we developed π-SeqOmics, a phenol-free workflow established through systematic benchmarking for the sequential isolation of DNA, RNA, and proteins from a single specimen, enabling integrated genomic, transcriptomic, proteomic, and phosphoproteomic analyses. Compared with conventional extraction and in-solution digestion workflows, π-SeqOmics achieves comparable proteomic and phosphoproteomic depth and reproducibility while preserving high-quality DNA and RNA for sequencing. The workflow performed robustly across a wide input range (5 × 10⁶–1 × 10⁵ cells) and multiple mouse tissues, consistently identifying over 8,000 proteins with strong quantitative reproducibility (r > 0.95). Together, these results establish π-SeqOmics as a standardized, practical, and cost-effective multi-omics sample preparation workflow for limited-input and biopsy-scale specimens, providing a robust foundation for systems biology and translational research.