2.1. Extracted Ion Chromatograms
To view extracted ion chromatograms, click the XIC menu and select XIC, or select the XIC icon in the toolbar.
Either action will open the XIC window.
To create a new XIC, click in the next available row (row 2 in this case). By default, the XIC is assigned to the next available “Window” meaning the data will appear in a new trace. By setting this to 0, the new trace would be overlaid on the first.
After entering parameters, hit OK.
The new XIC is displayed.
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“Save” and “Load” are used to save and load the contents of XIC windows in text format.
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“Scan Filters” will detect non-data dependent MS2 scans (i.e. targeted MS2 scans from appropriate experiments).
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To delete an XIC, click the tab on the upper left of the window (or click in the X column in the XIC window).
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The “Filter” indicates the type of data that will be selected for display. For example, one can choose MS1 data, MS2 data, or all data (for all data, the filter should be null or nothing entered). By default, some strings appear in the combo box by default (i.e. Full MS and Full MS2 for rawfiles or MGF ms2 for mgf files). Additional filters can be entered manually. To populate the combo box with targeted MS2 scans, hit the “scan filters” button.
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XICs can be deleted by selecting the “X” check box.
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Several types of scaling are possible. “Auto” automatically scales each chromatogram according to its maximum value. To scale a trace to another, enter “sX” where X corresponds to the window number to scale against. For example, to scale window 0 to the maximum intensity of window 1, s1 should be entered as window 0’s (row 1’s) scale parameter. Enter “max” to scale each XIC to the maximum of all displayed.
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XICs can also be overlaid by left click and drag from one window to another:
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Note the tabs that are displayed to the left of the XIC. Left click on the solid upper tab will delete the entire set of XICs. Additional sets of tabs are displayed for each XIC displayed in the window. Left click on the solid tab will make the trace “Active” – the apex intensity for this trace will appear to the left of the window, and the extracted mass range will appear above the window (in this example, two traces are displayed; XIC 610.995-611.102 is displayed in red; its max intensity is 4.7E7 counts). In addition, if peak integrations are perform, they will be performed on the active window. The +/- tabs are used to view/hide individual traces. The active trace cannot be hidden. The ‘>’ is used to send the individual trace to its own individual window.
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Another useful feature in the ‘XIC’ menu is ‘Propagate XICs’. This will display the same set of XICs for each data file that is currently open.
When wiff files are loaded, the different scan types in the data file are determined and will be entered as defaults in the filters combo box (For example, Exp 1 (Precursor), Exp 2 (ER), Exp 3 (EPI), etc.). These can be selected to perform XICs specific to particular scans.