In 2006, Kind and Fiehn released a database of all ‘correct’ molecular formulae of mass less than 500 u consisting of C, H, O, N, S and P^†. The list contains 1.6 million molecular formulae. Since this collection was calculated in silico, the exact isotopic mass and natural isotopic abundance of the molecule (M) is known to many decimal places. Using this database we determined the subset of molecular formulae that contained at least one hydrogen atom and, removing this atom, generated a list of M-H fragments; roughly doubling the number of entries.

Here it is interesting to note that with the removal of a hydrogen atom we have in effect generated a list of possible fragments where a single bond has been broken. Consider the case where a molecule is fragmented and a C-C bond is broken. Each fragment thus produced can be considered to be an M’-H species where the M’ corresponds to the fragment if it were to have had a hydrogen attached/removed rather than being part of a larger structure. Therefore one can consider the list of M-H species to be all possible fragments of the same set of atoms (CHONSP). It is trivial to consider adducts of M; M+H, M+Na, M+K and the masses of these are calculated on demand.

Our software package – Identity – allows the user to search the 3.2 million molecular formulae and adducts for a spectral feature in the range 1-500 u, in the domain of CHONSP, and view the isotope pattern of the species.

In addition, this software will display the isotope pattern of any other molecular formula, although this aspect does not determine whether the molecule is fully valent. The calculation of isotope patterns performed using the emass program detailed in a paper by Rockwood and Haimi.^‡ The licence for the emass software is below.

^†T. Kind, O. Fiehn, BMC Bioinformatics 2006, 7, 234. DOI: 10.1186/1471-2105-7-234
^‡A.L. Rockwood, P. Haimi, J. Am. Soc. Mass Spectrom. 2006, 17, 415–419 DOI: 10.1016/j.jasms.2005.12.001

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