MALDI-MS (matrix-assisted laser desorption/ionization mass spectrometry) is a popular technology for characterizing molecular compounds and their location within biological systems (e.g., tissues, microbial colonies, etc.) due to its high sensitivity and high throughput, relative to other spatially resolved MS technologies. In a typical workflow, peak assignments are based on matching the experimental masses to databases of masses for known molecules, either from parallel experiments or in silico prediction. To precisely match an entry in one of these databases, high resolution data with isotopic profiles are preferrable for high confidence identifications. Of particular interest for MALDI-MS analysis are proteins and their modified forms (proteoforms), which have roles in epigenetics (gene regulation), cell signaling, protein degradation, and signal transduction. However, only recently have developments addressing ion transmission and resolving power limitations enabled isotopically resolved MALDI-MS spectra for intact proteins (~<20 kDa). Therefore, most existing software for annotating MALDI-MS data is largely focused on molecules with relatively small isotopic profiles (e.g. lipids metabolites), with limited support for peptides (digested proteins). Consequently, users interested in peptide and protein MALDI-MS data often must manually combine the capabilities of several different tools for peak assignment, which is a time-consuming process.