TopMSV is a web-based tool for visualizing top-down MS data and the results of the spectral deconvolution tools TopFD and TopDIA and the proteoform identification tools TopPIC and TopMG. A dataset is the SQLite files of one run: TopFD or TopDIA writes the deconvoluted MS1 and MS/MS spectra and the MS1 3D peak levels into one file, and TopPIC or TopMG writes its identifications and the search database into a second file. After the files are uploaded through the browser, TopMSV generates all views on the fly: a raw-spectra browser with deconvoluted envelope annotations and linked navigation between MS1 scans and their fragmentation scans; protein, proteoform, and proteoform-spectrum-match (PrSM) views with annotated sequences, matched fragment ions, and spectra; a visual inspection calculator that matches a mass list against a protein sequence with chosen ion types, PTMs, and mass tolerance; and an interactive 3D view of MS1 peaks over m/z, retention time, and intensity.

The server side of TopMSV was developed using Node.js, Express.js, and TypeScript. It reads datasets directly from SQLite files and stores nothing derived on disk. The browser side was developed in TypeScript, in which 2D views of mass spectra and identified PrSMs were implemented using the D3.js library and the 3D view of LC–MS data using the three.js library.