MS Chromatogram window
On the GC/MS/MS-MS and LC/MS/MS-MS Instrument the standard Chromatogram window was replaced by MS Chromatogram window. The functionality of MS Chromatogram window differs slightly from the functionality of the Chromatogram window, but most of the functions are common between both windows.
Graph pane is divided into two parts in the MS Chromatogram window - original graph as in standard Chromatogram window, and the spectrum part displaying the spectrum at any given time or time interval. There is a special mode called MS Offsetting for displaying the signals in the MS Chromatogram window, allowing to offset different signals to the same baseline level while keeping the ratios of the signals, which can be set in the Graph Properties - Signals dialog invoked by using the Properties… command from the local menu. This setting helps to eliminate the background noise on some signals (notably TIC) for optical evaluation of correct ion ratios. The settings for the behavior of the spectral graph can be selected using the Graph Properties - MS Spectra dialog invoked by using the Properties… command from the local menu.
Signals in MS Extension
The number of signals displayed in the graph will change contextually as the user changes focus in the graph itself or select any signal or compound in the Result Table or on MS Method, MS Integration and Integration tabs. Each peak in the MS-MS Extension is defined by up to four EIC X - Reference m/z X Reference signals and a Quantification signal, which may be TIC, any of the Reference signals, sum of those or even an external signal. Different peaks may (and indeed will) differ in number of such defined signals and in the signals themselves - the EIC - reference m/z for them will differ too.
Order under which the signals are displayed is defined by the signals set in the System Configuration (and later Method Setup) that were used during the acquisition of the chromatogram. Standard signals defined in the System Configuration and Method Setup dialogs will be displayed first. Next, if a peak is selected, will be it's quantification signal, followed by the signals of reference ions. If one of the reference ions is at the same time used as a quantification signal, it will not be displayed for the second time. Next in order will be any signals displayed by the user manually from the raw data.
The standard signals behave exactly as the users are used to in Clarity, and they are saved when the chromatogram is saved. The rest of the signals are so called "Temporary Signals" created according to the information set in the MS Method and created always fresh from the raw data when they are needed. If an MS chromatogram is opened on non-MS Clarity Instrument, only the standard signals will be available for inspection and work, but the temporary signals will not.
Result Table
Another major change in the MS Chromatogram window touches the Result Table. On non-MS Instruments each signal has it's own Result Table, whereas on MS Instrument, the Result Table is common through all signals. The table header which normally changes color to match the color of the active signal is black on MS Instrument regardless of the signal selected.
The Result Table is a combination of two separate result tables - one created according to the MS Method Table, second one created according to the selected standard signal (Result Table Signal). The information on the signal used for this purpose is stored in the header of the table and can be changed by using the Result Table Signal option on the upper part of the MS Method tab.
Other changes in MS Chromatogram window
All changes in the MS Chromatogram window are described on particular places - MS menu, Result Table, Integration Table, MS Integration Table, MS Method tab, Import Chromatogram and the Graph Properties - MS Spectra tab.