How to plot an extracted ion chromatogram (XIC) in every GC-MS run

To follow one compound over a sequence, you extract the same ion from every run. In Nagura Lab that is one tick box: pick the ion once and it is plotted for every open run that has it.

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Plot the ion in every run

Open the runs: a folder of .D runs with .MS files, or the files themselves. The option below appears when two or more mass-spectrometry runs are open.
In the run list, click Explore spectra under the MS signal of one run. Click the chromatogram to see the mass spectrum at that time.
Pick the ion: click a peak in the mass spectrum, or type the m/z under the spectrum. The ± window (0.5 by default) sets how far from the m/z an ion still counts.
Tick in every open run and click Add chromatogram.

Each run gets a trace labeled with its run and the ion, for example orange.D · MSD1.MS XIC m/z 463. Runs that have no ion within the window are skipped; if none has it, Nagura Lab says so.

Compare the runs

Absolute and % of range switch between the real counts and a scale where every trace runs from 0% to 100%, which lines up peaks from runs with different amounts.
Drag across the chart to zoom into a time range; Reset zoom goes back.
Download CSV saves every plotted trace; Download PNG saves the figure with its legend.
Up to eight traces fit in one plot. If more would be added, Nagura Lab tells you how many it added.

Get numbers for the ion

For the retention time and area of that ion in every run, open Batch tools, choose MS: extracted ion chromatogram as the trace in the Window table, enter the same m/z and window, add a time window around the peak and click Calculate. See compare peaks across many runs.

Good to know

Nothing is uploaded. The ions are extracted in your browser.
The ion chromatogram in every open run works for up to 3 mass-spectrometry runs. For more it is free during early access with a verified email, for a limited time (details).
For the basics of a single GC-MS run (total ion chromatogram, spectra, one ion), see open an Agilent ChemStation .MS file.