ProtPipe2: Multi-Platform Downstream Proteomics Analysis Tool

Proteomics studies increasingly use different technologies, including mass spectrometry, the antibody-based Olink platform, and the aptamer-based SomaScan platform. However, downstream analysis often depends on platform-specific scripts or point-and-click tools, limits flexibility and makes analyses difficult to reuse across platforms. We developed ProtPipe2, a downstream proteomics analysis framework for mass spectrometry, Olink, and SomaScan data that is available as both an R package and an interactive web application. ProtPipe2 supports quality control, preprocessing, imputation, batch correction, statistical analysis, visualization, pathway analysis, and result export. ProtPipe2 expands the original Protpipe workflow to additional proteomics platforms and provides reusable R functions for imputation, batch correction, and other downstream analyses. Its redesigned web application provides user-controlled methods and parameters through the same R-based workflow. Case studies across mass spectrometry, Olink, and SomaScan datasets demonstrated a consistent downstream analysis workflow across platforms. By supporting three proteomics platforms through both graphical and scripted workflows, ProtPipe2 makes downstream analysis easier to perform, repeat, and review. ProtPipe2 is freely available at https://nih-card.github.io/ProtPipe2/.