Commands:
View > Ion Group
View > Unlink Ion Group
View > Charge State Determination
Sequences > m/z Chromatogram
A normalization ion group lists several chromatographic ions and allows to set their expected intensity. It is used to normalise chromatographic runs.
A Normalization Ion Group view is generated by using the command View > Normalization Ion Group. A Normalization Ion Group is used to normalize the ion intensities within chromatograms so that a set of norm ions has the same intensity in all of them. See Normalization for a detailed discussion of normalizations.
Activities:
- Adding or removing ions to the group by pressing the
button or by copying them from an Ion Group View.
- Determination of the ion volumes in a specific chromatogram: dropping the link icon
onto a chromatogram view.
- Filling in the Normalized Quantity column by typing in the values line by line or be selecting an ion volume volume and copy-pasting all values over to the Normalized Quantity column.
- Displaying the quantitative chromatogram, a chromatogram of a centroided, noise reduced ion: clicking onto the blue colored ion volume number of an ion
- Editing the ion volume number: displaying its chromatogram and changing its selection by ⌘ click-dragging over the chromatogram (only when the ion volume was determined by integration - see Arcadiate > Preferences… > Quantification: by integration).
- Re-establishing the default ion volume figure: clicking on a blue colored ion volume figure of the ion
- Display the m/z chromatogram of a selected ion: Sequences > m/z Chromatogram
- Unlinking the ion group from a chromatogram: command View > Unlink Ion Group
- Determining the ion volumes in several chromatograms: dropping the link icon
onto a chromatogram group whose chromatograms are aligned. The ion group has to be linked with a chromatogram that is part of the group to define the retention times of the ions in the other chromatograms.
- Charge state determination of ions in a chromatogram: the command View > Charge State Determination if the ion group is associated with a chromatogram
- Applying normalizations to chromatograms: after the ion group was linked to chromatograms their normalization factors had been calculated in the Norm-values Table. These values can be applied to the chromatograms by selecting the columns and pressing the
button.
- Removing the normalizations from chromatograms: Selecting the respective columns in the Norm-values Table and press the
button.
- Using Total Ion Count Normalization: Total ion count normalization is a function that the intensities in the chromatograms are multiplied by a factor which ensures that the total ion count of the normalized chromatograms is the same. The value in Arcadiate > Preferences… > Quantification: Normalize Chromatograms by their Integrated Ion Count defines the default value. For every specific normalization the function can be switched on or off in the Total Ion Count Normalization table.
- Visualizing and editing the normalization functions: linking the Ion Group Normalization view to a Data Graph view
displays the normalization function in the Data Graph view and allows editing.