Rate Analysis

The Rate analysis system is designed to facilitate the analysis of time dependent NMR properites. It can be used, for example, to extract relaxation rates or to visualize NOE build up curves. The procedure is used to analyze the intensities in a series of spectra collected with different mixing times. The analysis proceeds in a series of steps as follows:

  1. Peak pick the spectrum with highest intensities.
  2. Clean up peak lists.
  3. Open the Rate Analysis Panel.
  4. Set appropriate analysis parameters.
  5. Analyze each peak in list.

Peak pick spectrum with highest intensities.

Choose one spectrum to peak pick. For relaxation analysis this is typically the spectrum with shortest mixing time. For NOE buildup curves it is typically one with an intermediate mixing time.

Clean up peaks.

This step is not necessary, but it is useful to eliminate artifactual peaks at this stage. This is particularly relevant if all peaks are to be automatically analyzed. Any of the peak tools can be used for this step.

Open the Rate Analysis Panel.

Choose "Rate Analysis" from the Analysis Menu of the NMRView Control Panel. The following analysis panel will appear.

The "Rate Analysis Panel" consists of three portions:

  1. Data and Parameters
  2. XY Plot
  3. Spectrum Window

Set appropriate analysis parameters.

Matrix Prefix
The analysis system assumes the the datasets consist of a series of 2D spectra whose names can be decomposed into a prefix common to all spectra, and a unique descriptor for each spectrum. For example, T1_1.nv, T1_2.nv, T1_3.nv ..., or noe_0, noe_20, noe_40, ..., or T2a, T2b, T2c ... There is no requirement that the descriptors be numeric, or that the spectra be collected or numbered in any particular order. The prefix (T1_, T2, or noe_ in the above examples) should be entered into the field labeled "Matrix Prefix".
Standard Deviation
If confidence intervals for the extracted rates are to be estimated then a standard deviation for the noise in the spectrum must be entered. This can be estimated by placing the cursors on a peak free region of the spectrum and entering the "getval" command in the console window. Alternatively, some peaks can be fit as described below. The standard deviation of the data from the fitted line can be used as an estimate. As with this entire Rate Analysis system, it is up to the user to verify the statistical validity of this procedure. The estimated standard deviation should be entered into the field labeled "Std. Dev."
Intensity analysis mode
The estimation of the intensity of the peaks uses the "nv_peak analysis" command. This command returns various estimates of the peak intensity, including both peak height and peak volume values. The desired estimator type should be selected with the "Mode" menu. The default mode (Jitter) determines the height of the most intense point found within a certain range (+/- 25 % of the peak bounds) of the peak center. This allows for a certain level of variation of the peak position (i.e. jitter) from one spectrum to the next.
PeakList
The appropriate peaklist (created in the step above) should be selected from the peak list menu.
Descriptor/Time File
A file must be created containing the unique descriptor portions of the file names and the corresponding mixing times. The file should have the following format: 
descriptor time
descriptor time
etc.
For example: 
1  20
2 100
3 60
4 200
5 50
6 140
Times should be entered in ms. The file can have any unique name.
Setup
When the user clicks on the Setup button a File Open dialog will appear. The user should select the previously created Descriptor/Time file. The file will be read, the descriptor and time data will be displayed in the data table, and the appropriate datasets will be automatically opened if they have not been previously opened.
Non-linear fitting parameters
The parameters for the non-linear fit should be selected from the "FitPar" panel. This panel can be displayed by selecting the "FitPar..." button in the XY graph window.
Equation
Choose an equation appropriate to the experiment used to collect the data. An important descision is whether to use a two or three parameter fit. The three parameter fit, which includes a parameter to estimate the intensity at infinite time, might be considered by some to be the most appropriate mode. Unless, however, the data has very low noise, and long mixing times are included in the experimental data the two parameter fit, which assumes the value at long mixing times, often gives the most reasonable estimate of the amplitude and rate parameters. Again, it is up to the user to select and justify the most appropriate equation.
Confidence interval
Select a probability level to be used for the estimate of the confidence intervals of the fitted parameters. The confidence intervals are estimated using a Monte Carlo procedure.
Number of simulations
Select the number of simulations to be used in the Monte Carlo estimate of confidence intervals. There is no reason other than speed not to use the highest value (100).

Analyze the peaks.

The peak to be analyzed can be selected by entering a peak number in the Peak field, or by using the up/down buttons to navigate through the list. As each peak is selected, the peak intensities for that peak will be extracted from each dataset and displayed in the XY plot window. The spectrum window will show an expansion of the spectrum region containing the peak. The dataset used for the spectrum display can be changed by selecting the checkbutton next to the appropriate entry in the data table.

Fit
Click this button to perform the non-linear fit to the currently displayed data.
Fit All
Click this button to perform the non-linear fit to all the peaks. You will be prompted for a file in which to save the results.