Comment on “An Efficient Method to Calculate the Aggregated Isotopic Distribution and Exact Center-Masses” by Claesen et al

Claesen et al. [4] recently presented an efficient method for computing the isotope pattern of a molecule, that is, both the isotope distribution and the center masses (also called “probabilityweighted masses” and “aggregated isotopic variants” in [4]) of the isotope peaks. They favorably compare their approach against five other methods for simulating isotope patterns: Their tool BRAIN is more accurate than any other tool, and computation times are well below one second even for huge molecules of mass above 533403 Da and when computing 1325 peak masses. Unfortunately, the authors fail to mention SIRIUS [3] that is capable of performing such calculations, too. The user interface of SIRIUS does not offer to input a molecular formula, but the method is accessible through the source code freely available as open source.1 The mathematical details of the method were introduced in 2006 [2]. SIRIUS computations are based on the convolution of isotope distributions: In [2] it is proven that center masses, called “mean peak masses” in [2, 3], can also be computed via such convolutions. The same approach was independently, and somewhat informally, suggested in 2006 by Rockwood and Haimi [7]. Combining this with a smart Russian multiplication scheme allows us to quickly determine the isotope pattern of every element, which are then convoluted to determine the final isotope pattern of the molecule. The methods implemented in SIRIUS, including the decomposition of monoisotopic masses, are also available via the Bioconductor package “Rdisop” written by A. Pervukhin and S. Neumann.2 As default, SIRIUS uses the masses and abundances of isotopes from the AME2003 tables [1,9] and abundances from [5]. For the evaluations in this paper, we have instead used masses and abundances from the IUPAC 1997 standard [8], as it was done by Claesen et al.. We have evaluated SIRIUS on the same set of molecules [6], see Table 1 and Table 2 in [4]. For a fair comparison, we chose the number of computed center masses (mean peak masses) identical to those used in [4]. We found that the theoretical average masses of some molecules slightly differ from those reported in [4], with up to 0.000002 Da mass difference. To this end, we repeated all calculation of theoretical average masses with arbitrary high precision (BigDecimal type in Java) but ended up with the same