ProteoAnalyst: Connecting biological context and peptide-level evidence in quantitative proteomics and phosphoproteomics.

Abstract

Modern mass spectrometry now routinely quantifies thousands of proteins and phosphosites. While raw spectral processing and quantification have matured over the past few years, downstream statistical analysis and functional interpretation remain challenging. Current tools are often fragmented across separate applications for statistics, enrichment, network analysis, and phosphoproteomics. Furthermore, they operate largely at the protein or site level, leaving the supporting peptide, precursor, and phosphosite measurements out of reach; while pathway and network visualizations are provided without subcellular context. To address these limitations, we developed ProteoAnalyst, an easy-to-use web-based platform that takes common upstream outputs (MaxQuant, FragPipe, DIA-NN, and Spectronaut) through quality control, statistical analysis, and functional interpretation within a single environment. Researchers can navigate from pathways, compartment-aware interaction networks, and kinase-substrate networks down to the individual proteins, peptides, precursors, and phosphosites that support them. Dedicated modules extend this capacity to peptide-level detection of isoform usage and post-translational modification (PTM) relative fractions, phosphoproteomics with protein abundance correction, and biomarker analysis. Our benchmarks and case studies demonstrate that ProteoAnalyst integrates well-established methods with rich functional analysis and visualization to streamline data interpretation and hypothesis generation. ProteoAnalyst is freely available at www.proteoanalyst.ca.

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