Softwares for correction of MS data for natural abundance
Pierre Millard, University of Manchester (UK), INSA de Toulouse (FR)
10 December 2013
In your manuscript, you state that "only commercial software or user-specific approaches are available for the conversion of mass intensities (provided by the specific software implemented to the mass spectrometer) to the relative and molar isotopomer enrichments", and that "Before the implementation of LS-MIDA, [you] relied on the usage of a lab-specific Excel/Solver-based software". However, a series of free, open source, user friendly, multi-platform softwares for correction of MS-data have been published during the last decade. Among these software there is MSCorr (Wahl et al., Biotech Bioeng, 2004), an algorithm developed in Perl by (Moseley, BMC Bioinformatics, 2010), or IsoCor (Millard et al., Bioinformatics, 2012).
Although LS-MIDA may be of interest for some users, I think that other software also present original features. For instance MSCorr provides in-depth evaluation of errors, the Perl algorithm allows analytical correction of high-resolution MS-data, and IsoCor provides usefull options (correction of the label purity, correction for the occurrence of unlabeled positions in the label input, calculation of mean isotopic enrichment) and is also not restricted to 13C or 15N-labeling experiments. These software should be presented in your introduction to help potential users to choose the software which best suits their needs.
Softwares for correction of MS data for natural abundance
10 December 2013
In your manuscript, you state that "only commercial software or user-specific approaches are available for the conversion of mass intensities (provided by the specific software implemented to the mass spectrometer) to the relative and molar isotopomer enrichments", and that "Before the implementation of LS-MIDA, [you] relied on the usage of a lab-specific Excel/Solver-based software". However, a series of free, open source, user friendly, multi-platform softwares for correction of MS-data have been published during the last decade. Among these software there is MSCorr (Wahl et al., Biotech Bioeng, 2004), an algorithm developed in Perl by (Moseley, BMC Bioinformatics, 2010), or IsoCor (Millard et al., Bioinformatics, 2012).
Although LS-MIDA may be of interest for some users, I think that other software also present original features. For instance MSCorr provides in-depth evaluation of errors, the Perl algorithm allows analytical correction of high-resolution MS-data, and IsoCor provides usefull options (correction of the label purity, correction for the occurrence of unlabeled positions in the label input, calculation of mean isotopic enrichment) and is also not restricted to 13C or 15N-labeling experiments. These software should be presented in your introduction to help potential users to choose the software which best suits their needs.
Competing interests
No competing interests