Many protein isoforms -- arising from alternative splicing, post-translational modifications (PTMs), or paralogous genes -- have distinct biological functions. However, the accuracy of quantifying protein isoforms and their stoichiometries by existing mass--spectrometry (MS) methods remains limited because of noise due to variations in protein-digestion and in peptide-ionization. We eliminate the influence of this analytical noise by deriving a first-principles model (HIquant) for quantifying these stoichiometries only from corresponding-ion ratios. This approach allows unprecedented accuracy (error < 10%) in quantifying ratios between different proteins and their isoforms. I will discuss a mathematical proof of the conditions under which HIquant has a unique solution, and algorithms for its optimal solution.