Formulas of High MW Unknown Compounds from Accurate Mass Differences and Ranking of Best Candidates from First Principles

The number of possible candidate formulas for high molecular weight unknown compounds (e.g., 7000–8000 Da for common 20-mer oligonucleotides) by high-resolution mass spectrometry is in the order of several hundred thousand even at the highest level of experimental accuracy. In demanding analytical applications involving new chemistries and synthetic routes where little is known about the chemical nature or mechanisms of formation of the unknown compounds (e.g., impurities), the generation of a short list of the most plausible formulas would be highly desirable. Such an approach has been developed in the current work. The concept of mass difference from a reference compound is introduced to simplify the approach and greatly reduce the number of possible formulas. The approach allows for the generation of candidate formulas by both the addition and subtraction of atoms to account for all possible molecular changes from the parent compound. A reduction of 3 orders of magnitude in the number of possible formulas has been achieved by the approach. Ranking of the formulas by the product of the sums of the absolute changes in the total number of all atoms and all heteroatoms in the proposed difference formula successfully ranked the correct formula within the top 10 from a list of 200–250 best candidate formulas. There is a tendency for the impurities to be formed involving the least change in the number of atoms and heteroatoms. Δ_fH^o and Δ_fG′^o values can be used as a complementary ranking system of the top candidates. The approach is applicable to unknowns in any other systems of high MW compounds.