Here, we developed an R package called IsoMatchMS (Suite/IsoMatchMS) to support both the analysis of MALDI-MS data with molecular formula annotation, and the analysis of intact protein and peptide MALDI-MS data from ProForma 17 strings. IsoMatchMS derives molecular formulas from ProForma 17 strings or the modification formats from five different proteomics identification tools: MSPath-Finder 14 , ProSightPC 18 , pTop , TopPIC 20 , and MS-GF+. Then, IsomatchMS calculates full theoretical isotope profiles, matches them to a summed spectrum, and visualizes the overlap between the two in an HTML display (called a "trelliscope display") where each plot is an overlay of a single isotope profile for a molecule on the summed experimental spectra. Users can then sort the display by high-scoring distributions to confirm annotations. Unique to existing opensource software tools with functions to identify high-quality annotations, IsoMatchMS supports spectral summing, common proteomics datatypes (both peptide and intact protein), complex compounds with modifications and unknown mass shifts, any adducts with a known mass, and visualizes the results in highly shareable and sortable trelliscope displays. By unifying the analysis process for multiple types of biological molecules into a singular pipeline, IsoMatchMS reduces the time and effort for the annotation of MALDI-MS data.