Natural isotope correction improves analysis of protein modification dynamics

Stable isotope labelling in combination with high-resolution mass spectrometry approaches are increasingly used to analyze both metabolite and protein modification dynamics. To enable correct estimation of the resulting dynamics, it is critical to correct the measured values for naturally occurring stable isotopes, a process commonly called isotopologue correction or deconvolution. While the importance of isotopologue correction is well recognized in metabolomics, it has received far less attention in proteomics approaches. Although several tools exist that enable isotopologue correction of mass spectrometry data, the majority is tailored for the analysis of low molecular weight metabolites. We here present PICor which has been developed for isotopologue correction of complex isotope labelling experiments in proteomics or metabolomics and demonstrate the importance of appropriate correction for accurate determination of protein modifications dynamics, using histone acetylation as an example.

Automated summary

Stable isotope labelling combined with high-resolution mass spectrometry is increasingly used for analyzing metabolite and protein modification dynamics. Correcting for naturally occurring stable isotopes, known as isotopologue correction, is crucial for accurately estimating these dynamics. While tools exist for isotopologue correction in mass spectrometry data, they are mainly tailored for low molecular weight metabolites, prompting the development of PICor for complex isotope labelling experiments in proteomics or metabolomics.