We present a comprehensive Shiny application designed to create a library for Data-Independent Acquisition (DIA) by DIA-NN, a state-of-the-art software tool for proteomics data analysis. from Data-Dependent Acquisition (DDA) mzid files, and to facilitate the post-processing and visualization of DIA-NN DIA results.

This application integrates several critical functionalities into a user-friendly graphical interface, empowering users with minimal coding expertise to execute complex workflows. Key features include the parsing and extraction of relevant information at precursor and fragment ion levels from mzid files to construct high-quality DDA libraries, essential for accurate peptide identification in DIA workflows. Additionally, the application supports robust post-processing of DIA-NN output, including data normalization, filtering, and statistical analysis.

Additionally, our tool is providing interactive and customizable plots for matched MS/MS profile between DDA library and DIA data identified by DIA-NN. Moreover. Users may generate and download summary statistics, visualize protein and peptide quantification data, and perform comparative analyses between experimental conditions.

Our Shiny application offers a versatile solution for proteomics researchers, enhancing the reproducibility, accessibility, and efficiency of DDA library creation and DIA data analysis.