PalmLab: A Comprehensive Computational Platform for Systematic Annotation and Functional Interrogation of Protein Palmitoylation

Abstract

Protein palmitoylation is a dynamic and reversible post-translational lipid modification with progressively recognized pathophysiological relevance in cancer and a range of human diseases. Current databases, however, predominantly catalog palmitoylation sites derived from isolated literature reports, and suffer from a conspicuous lack of systematic harmonization across publicly available mass spectrometry (MS)-based palmitoylome datasets, which severely impedes standardized annotation and cross-cohort comparative analyses. Here, we introduce PalmLab, an integrative computational platform that synergistically couples MS-based palmitoylome data curation with interactive, multi-dimensional analytical functionalities for both human and mouse proteomes. Through a unified and rigorously standardized bioinformatics pipeline, PalmLab enables systematic reanalysis of all published palmitoylome datasets, yielding a curated compendium of 15,968 human and 9,924 mouse MS-validated palmitoylated proteins, a quantitative increase that more than doubles the total entries available in existing public repositories. The platform further provides user-friendly, code-free analytical modules that support differential palmitoylation profiling, context-specific pattern visualization, protein-protein correlation network inference, mutation-palmitoylation association mapping, and sequence-based motif discovery. Collectively, PalmLab constitutes a comprehensive and openly accessible resource for systematic palmitoylome mining and functional interrogation of palmitoylation events, thereby facilitating the elucidation of palmitoylation-mediated regulatory circuits and aiding the prioritization of novel therapeutic targets in oncology. The platform is freely available at https://palmlab.intelligent-oncology.com.