Package Design. IsoMatchMS was written in R 23 4.2.2 and has a main pipeline function which requires three inputs: 1) molecular formulas or ProForma 17 strings, 2) MS peak data, and 3) a settings file (an excel .xlsx). The molecular formulas or ProForma 17 strings need only be a vector of characters in R and thus can be read from any file format that can be read into R. Similarly, the MS peak data is a pspecterlib peak_data object that can be created from any two numeric vectors (m/z and intensity) or extracted from a mzML or a ThermoFisher raw file with a pspecterlib wrapper function, which uses mzR and rawrr. The settings file specifies several parameters such as m/z range and m/z error; examples are provided within the package. The run_isomatchms() function uses these objects to automatically perform the isotope calculations, peak matching, and trelliscope display generation.