The ProForma 17 strings can originate from experimental (e.g., LC-MS/MS) or protein sequence (e.g., UniProt 27 ) databases. If ProForma strings are not provided by an identification tool such as TopPIC , IsoMatchMS contains a function to derive them from mzid files generated by tools such as MS-GF+ or from various modification formats, including those used in the tools MSPathFinder 14 , ProSightPC 18 , and pTop. Molecular formulas are also accepted in lieu of ProForma strings, written simply as element and number of atoms with no spaces (e.g., "C2H5NO2"). MS1 spectra can be summed with other software (e.g., instrument vendor software), or calculated from mzML files with IsoMatchMS. Within the settings files, users can set a variety of parameters to optimize performance, including the isotope algorithm to use (either Rdisop 28 or isopat ), range of m/z values to search, an abundance noise filter, a minimum number of isotopic peaks to identify, a maximum number of charge states to investigate, and PPM and abundance tolerances to be considered a "match." The example settings files in IsoMatchMS contain more details about each parameter, along with suggested defaults. For intact protein datasets, we suggest a minimum of 5 identified isotopes, higher noise filters (2.5-10%), and using the Rdisop 28 isotoping algorithm due to its higher precision at heavier masses. For smaller isotope profiles, we suggest a minimum of 2 identified isotopes and lower noise filters (0-2.5%). Available isotope scores include Pearson correlation and the absolute relative error (1) where AM is the measured abundance, AC is the calculated abundance, and n is the number of peaks.