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By determining two dimensions in chemical space (the C and N count) the degeneracy of possible formulae is reduced.
The astronomical number of possible formulae means that heuristic limitations are required to guide this combinatorial search.
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SBMLsqueezer takes all this information into account and provides a contextual selection of possible formulas for each particular reaction within the model.
Accurate masses enable one to determine the right elemental formula among different possibilities at a given nominal value or at least to significantly reduce the number of possible formulas [ 42].
For small molecule metabolites, maximal values for these dimensions might be close to 200 carbons and hydrogens, and lesser numbers of heteroatoms (see Materials and Methods), which still allows for a search space of 288,120,000 possible formulae.
The development of certain heuristics for prioritizing the likelihood of chemical formulae reduces the number of possible chemical formulae, but leaves some ambiguity that can be reduced through additional experimentation [ 11, 12].
Thus, formula generators must explore all possible formulae of the form C aH bN cO xS yP z, which spans a six dimensional space, where the dimensions are a, b, c, x, y, and z.
Due to the large number of possible chemical formulae associated with this mass value, biological inference is impractical.
The most common approach begins with combinatorial generation of possible chemical formulae that might correspond to a detected mass spectral feature.
Other information embedded in mass spectral data can serve as non-mass-based criteria to restrict the range of possible chemical formulae.
Furthermore, to test whether SIL knowledge was able to reduce the degeneracy better than the ratios of isotopic peak intensities, the number of possible chemical formulae remaining when the N and C count are known was also determined.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com