PTMsite-Finder supports DIA-NN-based PTM DIA proteomics

we developed PTMsite-Finder, a user-friendly graphical interface software tool designed to report and quantify multiple PTM sites directly from DIA-NN outputs. We validated PTMsite-Finder’s phosphosite quantification accuracy for phosphoproteomics DIA-MS data and demonstrated its versatility in processing various PTM types, including ubiquitinomics, acetylomics, and biotinylation diaPASEF data. Additionally, PTMsite-Finder outputs are compatible with kinase prediction and PTM site motif analysis tools. Altogether, PTMsite-Finder is a robust and versatile tool for analyzing DIA-NN outputs across multiple types of DIA-MS data.