Integration
Invoking this command switches the results panel of the Chromatogram window to the Integration tab, which contains the selector of the integration algorithm and the Integration Table.
When using a multi-detector chromatogram, the selection of the integration algorithm is common for all signals in the chromatogram but the Integration Table is always displayed for the active signal (the color of the table header corresponds to the color of the signal and signal name is contained within).
The content of the tab is based on the Integration tab of the method used to measure the chromatogram. These values can be further modified through operations available in the Chromatogram window in the toolbar or the Chromatogram menu.
Selects the integration algorithm for integration of displayed chromatogram. It is common to all signals.
Currently Clarity offers two different integration algorithm lines - Wave and Legacy. Both lines differ in the approach to the automated integration and both have their strong sides and drawbacks. Some functions of the integration algorithm may be only present in particular versions of integration algorithm. The default integration algorithm for newly created methods is Legacy, the algorithm in newly measured chromatograms is based on algorithm selected in the method.
Note:
In case the selected integration algorithm fails to solve the integration of your chromatograms, we suggest to try the other one to see whether the situation will be better.
In case the chromatogram is opened with the stored method (historical version of the method) and the integration algorithm used by Clarity changed after it's creation, the Integration Algorithm dropdown will contain three integration algorithm versions - newest Legacy version, newest Wave version and the historical algorithm used in the chromatogram (be it Legacy or Wave, selected). To distinguish the historical version from the latest in the given line, the descriptions will contain the revision used for both. Upon editing the chromatogram, the algorithm will change to the latest version of the given line and will not be able to be changed back.
Integration table
The integration table records all operations performed on the baseline and peaks. The header of the table contains information on the chromatogram, particular signal and integration algorithm version used. The information is printed along with the integration table when the table is selected for printing.
Selects the operations to be performed on the chromatogram. Clicking the right border of the field displays a list of all possible operations (identical to the list of commands from the Chromatogram - Baseline, Peak, Integration, Separation and other sub-menus in the Chromatogram window).
Chromatogram - Integration
a) Indicates the starting time of the operation (for interval commands).
b) Indicates the peak retention time (for commands that modify the peak start, peak end, etc.).
a) Indicates the final time of the operation (for interval commands).
b) Indicates the position of a new start, end, etc. relative to the peak apex (for commands that modify the start, end, etc.).
Note:
Zero entered in the Time B for interval operations will set the end of the interval to the end of the chromatogram.
Note:
Indicating the relative position (i.e. time) is more suitable than indicating a mere absolute value, since in using the Integration Table the peak with the most similar retention time is then found and the peak start/end is shifted to the point calculated from the relative shift on the actual retention time. This substantially diminishes the differences in actual retention time of the same peak in different chromatograms.
Value (if relevant for the operation) with appropriate units.
Description of fields of integration table
Global Peak Width / Local Peak Width [min]
This parameter defines the smallest peak width, which is to be detected. The value range is between 0,001 and 10 minutes.
The value is not critical, so even narrower peaks than the entered value will be detected, but if set incorrectly, the beginning and end of a peak may be inaccurately determined and the baseline could be incorrectly inset.
The Global Peak Width parameter is always displayed in the first row of the integration table and is applied to the whole chromatogram.
It is possible to set a different peak width for individual sections by adding the Local Peak Width parameters into further rows of the integration table which then override the Global Peak Width settings in the given area of chromatogram.
Global Threshold / Local Threshold [mV]
Determines the sensitivity the integration algorithm has to noise. The height of all peaks (measured from the baseline to the top) that should be detected has to be at least double this parameter. The value range must be 1 µV -10 V.
The Global Threshold parameter is always displayed in the second row of the integration table and is applied to the whole chromatogram.
It is possible to set a different noise threshold for individual sections by adding the Local Threshold parameters into further rows of the integration table which then override the Global Threshold parameter in the given area of the chromatogram.
Sets the averaging of data points for the signal displayed (and calculated with) in the chromatogram. Global Filter - Bunching serves as a filter and reduces the high frequency noise. The value must be between 1 (no averaging performed) and 250 (for each 250 data points measured, only 1 is displayed). Applying higher Global Bunching values will significantly change the signal course.
Global Filter - Bunching parameter is always displayed in the third row of the integration table and is applied to the whole chromatogram.
Global Baseline Slope / Local Baseline Slope
Determines the position of the peak starts and peak ends on peak sides. The value must be between 0 and infinity, the higher the value the higher on the peak slope the starts and ends will be. If the value is set to 0, default peak start and peak end position is used (the value is considered to be 8*Global Threshold. The slope on peak ends is considered as a negative value of the value entered, target slopes for negative peaks are using negative value for starts and positive one for peak ends.
Global Baseline Slope parameter is always displayed in the fourth row of the integration table and is applied to the whole chromatogram. It is only present for Wave algorithm.
It is possible to set a different slope for peak starts/ends for individual sections by adding the Local Baseline Slope parameters into further rows of the integration table which then override the Global Baseline Slope parameter in the given area of the chromatogram.
Limits the time period over which the chromatogram will be integrated. This means that the chromatogram profile will be ignored beyond the set time interval. This is the main difference compared to Lock command, which cancels already integrated peaks only in defined sections and does not reintegrate the whole chromatogram. If the parameter is not defined, integration is done on the whole chromatogram.
Enables the detection of negative peaks. If this function has not been enabled, all negative peaks are considered to be correct course of the baseline (in a similar way as removing the peak with the use of Reject Negative function).
This parameter sets the minimum peak area in mV.s. Peaks whose area is smaller than the specified value are not displayed.
This parameter gives the minimum peak height in mV. Peaks whose height is smaller than the specified value are not displayed.
This parameter gives the minimum peak half-width in minutes. Peaks whose W05 is smaller or equal to the specified value are not integrated.
Specifies the maximum slope of the baseline. If the baseline slope is smaller than the specified value, the separating perpendicular line is canceled and the baseline passes through the valley. The default value of 0 prevents the baseline from passing through the valley.
Constitutes the first condition imposed on tangential separation. The condition is satisfied if the ratio of areas of the separated and the main peak exceeds the specified value.
The value of 0 prevents tangential separation. If this operation is selected in the Integration table, its value is set to value of 10 and in general increasing value causes higher degree of tangential separation of the raider peaks. If there is no Tangent Slope Ratio item defined in the Integration table but Tangent Area Ratio is defined, the value of the Tangent Slope Ratio is considered to be 10.
This is the second condition imposed on tangential separation. The condition is satisfied if the ratio of slopes of the second and the first peak exceeds the specified value. The slope ratio is defined as the tangent to the first peak at its end point divided into the slope of the line connecting the beginning and end of the second peak.
Value of 0 prevents tangential separation. If this operation is selected in the Integration table, its value is set to value of 10 and in general increasing value causes lower degree of tangential separation of the raider peaks. If there is no Tangent Area Ratio item defined in the Integration table but Tangent Slope Ratio is defined, but the value of the Tangent Area Ratio is considered to be 10.
Commands from Chromatogram - Integration menu:
FFT, Savitzky-Golay, Spike, Moving Average. A detailed description of these functions is provided in the chapter "Integration"
Commands from Chromatogram - Baseline menu:
Lock, Valley, Together, Forward Horizontal, Backward Horizontal, Front tangent, Tail tangent, Clamp Negative, Cut Negative, Reject Negative, Allow Crossing, Spike Removal. A detailed description of these functions is provided in the chapter "Baseline"
Commands from Chromatogram - Peak menu:
Start, End, Both, Add Positive, Add Negative, Force Peak Name, Solvent Peak. A detailed description of these functions is provided in the chapter "Peak"
Adds (Add group) and removes (Delete group) a group of peaks. A detailed description of these functions is provided in the chapter "Peak"
Commands from Chromatogram - Noise & Drift menu:
Noise, Drift, ASTM Noise, 6-Sigma Noise. A detailed description of these functions is provided in the chapter "Noise & Drift"
Sequence of evaluation
The evaluation process does not proceed exactly in the same order as the parameters in the integration table are shown. The process is:
- Primarily initiated with the Global (Local) Peak Width, Global (Local) Threshold, Integration Interval and Detect Negative parameters.
- Secondly the ValleyToValley Slope parameter will be applied. After all groups of non-resolved peaks have been tested by this parameter the remaining two parameters Tangent Area Ratio and Tangent Slope Ratio are applied to all remaining non-resolved groups. Tangential separation is used whenever the relevant criteria are met.
- Only then is the Integration Table used, followed by the Rejections parameters.
It thus follows that the separation parameters are not applied (e.g. to manually added peaks) and can be suppressed by the Together and Valley commands included in the Integration table.
Paste (CTRL+V) into the Integration Table
Inserting into the Integration Table using the Paste command or using the keyboard shortcut CTRL+V is possible with some limitations - it is only possible to copy non-global lines of the Integration Table as a whole. It is not possible to paste global lines, overwrite only particular lines or just selected values. When the Paste operation is invoked for the Integration Table, Clarity evaluates the content of the clipboard on correctness. Incorrect clipboard content is announced by an error message and Paste operation fails, while on correct evaluation the focus in the Integration Table is moved to the empty edit line and the rows from the clipboard are added to the end of the Integration Table.
Note:
Typical fails in evaluation of the correctness of the Integration Table may be too few columns in the clipboard, global operations in the clipboard or units inside of the value cells of some rows while copying from text file or Excel.
You may consider using one of the alternative approaches of copying the Integration Table, as described in the section Method - more specifically the Set Model, Copy from Model and Copy from Chromatogram commands.