MASH Explorer App is a universal, comprehensive, and user-friendly software desktop environment for top-down proteomics. It can process top-down high-resolution MS and LC-MS/MS data from various vendor formats (Thermo .raw, Bruker .baf and .ascii, Waters .raw directory, and universal data file formats .mgf and .mzXML) with multiple spectral deconvolution and database searching algorithms. Within the software, graphical tools are implemented to allow users to manually explore the peak picking, deconvolution, and search results, to investigate overlooked fragment ions, and to combine LC-MS/MS spectra.It is developed by an interdisciplinary team consisting of experts in top-down mass spectrometry-based proteomics, computational data science, and bioinformatics/biostatistics.