IntroToIntegration

Integration is performed in MonoScope using Peaklists.

Peaklists can be created in MonoScope in several ways:

1. Importing a peaklist into MonoScope from an external file using "Peaks-Import Peaklist"
2. Create a new peaklist using the MonoScope menu "Peaks-new peaklist".
3. Just start picking peaks in MonoScope. A new peaklist is generated automatically. Don't forget to "Peaks-Add to repository" before you close MonoScope.
4. Generate a peaklist from HomoScope based on the displayed crosses using "File-Export Peaks to MonoScope"
5. Generate a peaklist from PolyScope based on the displayed crosses
   • in the plane using "File-Export Plane Peaks to MonoScope"
   • in the strips using "File-Export Strip Peaks to MonoScope"
6. Generate a peaklist based on assignments in the SpinSystems? from a script like PeakListNumberedByResidue?.lua

When you create a peaklist it is associated with the spectrum where you created it. The spectrum "owns" the PeakList?.

Once you have created a peaklist it will appear in the CaraExplorer under Peaklists. Here you can see which spectrum owns the peaklist. You can open the peaklist with its owner spectrum in one of several ways.

1. Right-Click on the Peaklist in the Cara Explorer under Peaklists and select "Open MonoScope".
2. Open the owner spectrum with MonoScope from the CaraExplorer under Spectra. In MonoScope open the leaklist using "Peaks-Open Peaklist"

Next, the Peak Model is "tuned".

1. Click on a well-resolved and representative peak and zoom in to it.
2. Integrator-Show Base Width
3. Integrator-Show Peak Model
4. Integrator-Tune Peak Model. Adjust the sliders for width x and width y to match the 1D profiles of the peak.

The PeakModel affects the results of the integration and this depends on the integration method.

Center peaks on their maxima.

1. Show peaklist with "sl" or "view-show list".
2. Double-click on a peak. (Start with the first one in the list)
3. Adjust the cursor position onto the maximum with the arrow keys.
4. Type "mp" to move peak or rightclick "move peak".
5. Repeat steps 2-4 until all peaks are centered.
6. During peak-centering you may find that you want to adjust the Peak model. Keep in mind that a single model is applied to ALL peaks. You cannot adjust the peak model for each peak. (Actually, CARA allows multiple peak-models but there is no graphic interface available to separately adjust them. It must be edited in the repository).

Select the Integration mode.

Integrator-Integration Method-

• Model-based linear equation system: this is a linear deconvolution of intensities. Unfortunately it occasionally returns unrealistic intensities if peaks are very close to eachother. See Issue 0639 and IntegratorIssues for additional suggestions.
• Base rectangle Intensity Sum to integrate a rectangular region whose dimensions are determined by the PeakWidths? of the PeakModel.

Integrate!

1. Integrator-Update all amplitudes
2. Integrator-Integrate all

Sorting the peaklist:

The amplitudes and volumes appear in separate columns of the peaklist. You can sort by either column by clicking at the top. This way you can find very intense peaks or very weak peaks that may need inspection or removal.

Navigation:

1. Double-click on a peak in the peaklist to move the cursor onto the peak and select it.
2. Click on a peak and type "sp" to show the peak in the peaklist.
3. select several peaks by Shift-click-dragging a box around them.

Shortcuts:

1. "mp" move peak
2. "dp" delete peaks

Writing out integrals:

1. Right-Click on the peaklist and select "Export peaklist" to write out a XEASY format peaklist
2. Right-Click on the peaklist and select "Export table" to write out the peaklist in spreadsheet format.
3. You can do the same thing using the menu "Peaks-Export peaklist" and "Peaks-Export Integration Table".

Note that Integration Table also works for a series of spectra integrated in a Batch List.

Advanced Topics:

How to apply BatchIntegration to a series of spectra.

Back to HomonuclearAssignment

Next to StructureCalculation