MS Chromatogram window

On the GC-MS and LC-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.

Spectral graph

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.

The spectral section of the graph displays the currently relevant spectral information. If there are multiple spectral information stored within chromatogram, these can be switched between using the Select Spectral Data drop-down in the MS toolbar. The visible spectra (including possibly also the active spectral data) change when a fresh compound is selected, either through selecting it in the chromatogram graph, Result table or MS Method Table. In this case, if the identity confirmation with the spectral library search is used, the spectrum is overlying the library spectrum of the expected compound. The spectrum for any part of the chromatogram can be displayed through MS - Show Spectrum command. Which spectrum is currently displayed may be discerned from the legend of the spectral graph, showing the range of time for which the spectrum is valid.

Basic display of the spectral graph shows the dependency of relative intensity (intensity normalized to the most intense m/z ion) on the m/z value, but the display can be changed through the Graph Properties - MS Spectra dialog invoked by using the Properties… command from the local menu. The relative intensity can be changed to absolute, the description of the m/z sticks in-graph may be changed as well.

There is a special mode called MS Offsetting for displaying the signals in the graph of MS Chromatogram window, allowing to visually 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.

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 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 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.

View Menu

Maximize Spectrum

The command maximizes the spectrum to cover the entire window (hides the bottom tabs). Double click near the splitter (the cursor will change to ) to achieve the same effect.

Show All

The command restores default view showing chromatogram, spectrum and the bottom tabs.

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.