ProteoScanner is an intuitive and versatile open-source software platform that offers an integrated approach for proteomics data analysis. With a focus on user-centric design, it facilitates an end-to-end workflow that encompasses data preparation, pre-processing, statistical testing, visualization, and biological interpretation. The incorporation of various statistical analyses and visualization tools allows for a sophisticated yet straightforward examination of complex datasets, ensuring that users can easily navigate through the analytical process. The software is an open-source, which allows full tweaking capabilities that can be summarized in transparency, flexibility, community-driven development, customizability, interoperability and long-term viability. It is compatible with different data array from current mass spectrometry equipment (Sciex and Thermo). This flexibility is further enhanced by the software’s foundation in Python and R, exploiting the capabilities of the two languages. ProteoScanner has a standardized quality and efficiency in producing comprehensive representations and biological insights. Combining a user-friendly interface with the required analytical depth, It stands as a testament to the software’s commitment to facilitating scientific discovery, providing researchers with a comprehensive as well as an intuitive tool in use. This balance of sophistication and accessibility makes ProteoScanner an invaluable resource for the omics research community. It is available as downloadable, executable file.