Peak-tracking for stepwise perturbed NMR spectra: development of a new analysis method

Stepwise perturbed NMR spectra analysis is a powerful tool capable of describing kinetic, thermodynamic, structural aspects of proteins at a residue level and of following the physical and chemical changes of the system. The analysis of an NMR spectrum still offers compelling challenges to the automatic identification of the chemical shift evolution. We designed and developed a data-analysis method which allows automatic peak detection in every spectrum, peak tracking between spectra and peak reconstruction for BLUU-Tramp sessions, a stepwise isotopic exchange experiment producing few hundreds of 2D NMR spectra. The method has been named TinT (Trace in Track), referring to the idea that a gaussian decomposition traces peaks within the tracks recognized through 3D mathematical morphology. TinT is capable of determining the evolution of the chemical shifts, intensity and linewidths of each tracked peak. The performances obtained in term of track reconstruction and correct assignment on realistic synthetic spectra were high above 90% when a noise level similar to that of experimental data were considered. TinT was applied successfully to several protein systems during a temperature ramp in isotope exchange experiments. The comparison with a state-of-the-art algorithm showed very good results for great numbers of spectra and low signal to noise ratios, when the graduality of the perturbation is appropriate. In the thesis, in addition to the description of the current version of TinT, some observations and considerations that can allow future revisions or improvements on BLUU-Tramp protocol or its analysis are also described.