A computer programme 'PolyCut' has been written to assist mass spectrometry-based bioinorganic studies via top-down and bottom-up approaches in positive and negative ion modes. PolyCut is designed to cope with metalloproteins, metallo-polymers and biomolecules with heavy element(s) as one (or more) of the charging agents at defined but different oxidation states. It does automatic assignment by considering the entire experimental and simulated isotopic patterns of an ion rather than reading only the mono-isotopic and average m/z values (and/or mass values). The calculation of chemical formula and the simulation of isotopic pattern for an ion at various charge states require PolyCut to be informed of the user-defined elements, the user-defined abundance of isotopes for each element, the user-defined oxidation state of an element, the user-defined residues and sequence of a polymer, and the user-defined fragmentation (or digestion). The programme successfully assisted MSn studies of two copper proteins coordinated to platinum(II) centres (a functional group possessing an intrinsic positive charge rather than a neutral organic modification), published as J. Biol. Inorg. Chem. 2009, 14(2), 163-165; Metallomics 2013, 5(8), 946-954. Besides polypeptides, polynucleotides and polysaccharides, PolyCut can be extended to other polymers using user-defined monomer residues.