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We would like to thank Professor Böcker for pointing out the omission of the SIRIUS software in the comparisons presented in our paper [1]. Indeed, we did miss this method as it was not published in a mass-spectrometry-related journal, but as a manuscript in the “Gene Expression” section of the Bioinformatics journal. We do appreciate that Professor Böcker supplemented our paper by reporting the results of a comparison of SIRIUS and our method. It is reassuring that the results indicate a comparable performance of SIRIUS and BRAIN in terms of accuracy and running times.
The very small differences in the theoretical average mass of molecules (6), (8), (9) and (10), pointed out by Professor Böcker, are due to a wrongly reported Table 1 in our article [1]. We mistakenly assumed that the NIST [2] values used by IsoDalton [3] were identical to the IUPAC 1997 standard (Table 1). However, this confusion did not influence the comparison between BRAIN and the other methods reported in our paper, as all the abundances and masses in our comparison were changed to the values used by IsoDalton [3].
In fact, the reported differences in average mass illustrate the sensitivity of the isotopic distribution calculations to the used mass and abundance probability values of the elemental isotopes. Even for very small differences in mass between NIST and IUPAC1997, the isotopic distribution and mass-centers of large molecules (heavier than 50 kDa, say) are influenced. For larger fluctuations of the masses and/or abundances of elemental isotopes, the effect on the isotopic distribution is even more pronounced and, in some cases, becomes troubling, as illustrated in Tables 2 and 3. The tables show the differences between the theoretical mono-isotopic masses (Equation 24 in [1]) and theoretical average masses (Equation 25 in [1]) of 10 molecules [1] based upon the default isotope information used by BRAIN [1] and IsoDalton [3] (NIST), the IUPAC1997 standard [4], IsoPro [5], Mercury [6] and Emass [7], and NeutronCluster [8] (Table S1 in [1]).
The differences between the theoretical average masses of molecule (10) vary from 0.000002 Da (IUPAC1997) to 50.007462 Da (isotope information of NeutronCluster), which is no longer ignorable. For extremely large molecules, this will be also the case for the mono-isotopic masses.
By this sensitivity analysis, we can conclude that deviations of the elemental isotope abundance values and/or isotope masses do have a large influence on the average mass of the molecule.
Finally, we also acknowledge that the molecular formula of molecule (7), reported in Table 2 of our article, is missing 40 sulfur atoms. However, the correct atomic composition was used in our calculations.
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