We describe a new algorithmic approach able to automatically pick and track the NMR resonances of a large number of 2D NMR spectra acquired during a stepwise variation of a physical parameter. The method has been named Trace in Track (TinT), referring to the idea that a gaussian decomposition traces peaks within the tracks recognised through 3D mathematical morphology. It 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. A comparison with a state-of-the-art algorithm showed promising results for great numbers of spectra and low signal to noise ratios, when the graduality of the perturbation is appropriate. TinT can be applied to different kinds of high throughput chemical shift mapping experiments, with quasi-continuous variations, in which a quantitative automated recognition is crucial.
[NMR paper] VirtualSpectrum, a tool for simulating peak list for multi-dimensional NMR spectra.
VirtualSpectrum, a tool for simulating peak list for multi-dimensional NMR spectra.
Related Articles VirtualSpectrum, a tool for simulating peak list for multi-dimensional NMR spectra.
J Biomol NMR. 2014 Aug 14;
Authors: Nielsen JT, Nielsen NC
Abstract
NMR spectroscopy is a widely used technique for characterizing the structure and dynamics of macromolecules. Often large amounts of NMR data are required to characterize the structure of proteins. To save valuable time and resources on data acquisition, simulated data is useful in...
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08-15-2014 12:53 PM
VirtualSpectrum, a tool for simulating peak list for multi-dimensional NMR spectra
VirtualSpectrum, a tool for simulating peak list for multi-dimensional NMR spectra
Abstract
NMR spectroscopy is a widely used technique for characterizing the structure and dynamics of macromolecules. Often large amounts of NMR data are required to characterize the structure of proteins. To save valuable time and resources on data acquisition, simulated data is useful in the developmental phase, for data analysis, and for comparison with experimental data. However, existing tools for this purpose can be difficult to use, are sometimes specialized for...
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08-13-2014 07:50 PM
[NMR paper] Bayesian Peak Picking for NMR Spectra.
Bayesian Peak Picking for NMR Spectra.
Related Articles Bayesian Peak Picking for NMR Spectra.
Genomics Proteomics Bioinformatics. 2013 Oct 31;
Authors: Cheng Y, Gao X, Liang F
Abstract
Protein structure determination is a very important topic in structural genomics, which helps people to understand varieties of biological functions such as protein-protein interactions, protein-DNA interactions and so on. Nowadays, nuclear magnetic resonance (NMR) has often been used to determine the three-dimensional structures of protein in vivo. This...
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11-05-2013 06:53 PM
Stepwise Filtering of the Internal Layers of Dendrimersby Transverse-Relaxation-Edited NMR
Stepwise Filtering of the Internal Layers of Dendrimersby Transverse-Relaxation-Edited NMR
Luiz F. Pinto, Ricardo Riguera and Eduardo Fernandez-Megia
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja4059348/aop/images/medium/ja-2013-059348_0007.gif
Journal of the American Chemical Society
DOI: 10.1021/ja4059348
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/ipXC3MPLDn8
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07-30-2013 09:57 PM
[NMR paper] Prediction of peak overlap in NMR spectra.
Prediction of peak overlap in NMR spectra.
Related Articles Prediction of peak overlap in NMR spectra.
J Biomol NMR. 2013 Apr 13;
Authors: Hefke F, Schmucki R, Güntert P
Abstract
Peak overlap is one of the major factors complicating the analysis of biomolecular NMR spectra. We present a general method for predicting the extent of peak overlap in multidimensional NMR spectra and its validation using both, experimental data sets and Monte Carlo simulation. The method is based on knowledge of the magnetization transfer pathways of the NMR...
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04-16-2013 07:46 PM
[NMRpipe Yahoo group] Problem peak-picking 3D spectra
Problem peak-picking 3D spectra
Hello All, I've been trying to run the automated peak detection, but I've run into some difficulty. Picking a slice from a 3D spectrum works without problems,
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05-27-2011 10:40 AM
[NMR analysis blog] Intelligent Peak Picking of 1D NMR Spectra
Intelligent Peak Picking of 1D NMR Spectra
In case you hadn´t noticed, version 7 of Mnova was released just a few days ago.
Whilst this new version presents a number of significant improvements in the software, in this post I would like to focus on a new peak picking concept which, to the best of my knowledge, is novel and in some way, revolutionary. I will try to keep this as short and clear as possible, just to illustrate the very basic ideas that motivated this new approach to peak picking. In the next posts I will elaborate further on some of the new points introduced here.
...
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05-16-2011 08:23 PM
[NMR paper] Automated peak picking and peak integration in macromolecular NMR spectra using AUTOP
Automated peak picking and peak integration in macromolecular NMR spectra using AUTOPSY.
Related Articles Automated peak picking and peak integration in macromolecular NMR spectra using AUTOPSY.
J Magn Reson. 1998 Dec;135(2):288-97
Authors: Koradi R, Billeter M, Engeli M, Güntert P, Wüthrich K
A new approach for automated peak picking of multidimensional protein NMR spectra with strong overlap is introduced, which makes use of the program AUTOPSY (automated peak picking for NMR spectroscopy). The main elements of this program are a novel...
Automation of peak-tracking analysis of stepwise perturbed NMR spectra
Linear Mode
