How to compare peak height, area and retention time across many runs

Is the retention time drifting? Is the area of the standard stable over the sequence? Both questions need the same peak, in every run, in one table. The window table does that for a whole folder of runs at once.

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What the window table does

You choose a trace and set one or more time windows around the peaks you follow. For every run, Nagura Lab reports the highest point in each window, its retention time and the area. It is plain arithmetic over the data points, with no automatic peak detection, so every number can be checked by hand. For automatic peak finding and boundaries you adjust on the chart, see how peak integration works.

Make the table

Open the runs, for example a whole folder (see export a whole sequence). Scroll to Batch tools and the Window table.
Choose the Trace. The list shows every signal found in the runs and in how many of them. You can also pick a chromatogram at a wavelength from diode-array data (type the wavelength in nm), the total ion chromatogram, or an extracted ion chromatogram (type the m/z and the ± window). Runs that do not have the trace are left out, and the card says how many.
Click Add window and type the start and end in minutes, or zoom the chart onto a peak and click Add zoomed range of the chart to copy the time range you see. Rename a window to the compound. Add one window per peak.
Click Calculate. Every run gets one row per window.
Click Download window table (CSV) to save nagura-window-table.csv for Excel, Origin, Python or R.

What the columns mean

RT at max (min): the time of the highest point in the window. Compare it across runs to see retention time drift.
Max: the value of that highest point, in the unit of the trace (the CSV has a Unit column).
Area (unit·s): the area under the signal between the start and end of the window, by the trapezoid rule, with time in seconds as chromatography data systems report it.
Area above baseline (unit·s): the same area after taking away a straight line from the first to the last point of the window. Put the window edges on the baseline on both sides of the peak.
Points: how many data points fall inside the window. A window with fewer than two points has no area.

The CSV also has the sample, the trace name and the window start and end next to each row.

Keep windows tight

A window counts everything inside it, not only the peak. If it is wide, or the baseline drifts across it, the plain area can even come out negative. Keep each window just around its peak, and check one or two runs against your data system before you rely on the numbers. This is not validated software: for regulated work, use your validated system.

Good to know

Nothing is uploaded. The numbers are calculated in your browser.
The batch tools work on your first 3 runs. For more runs they are free during early access with a verified email, for a limited time (details).
To overlay the same runs on one chart first, see compare and overlay several HPLC runs.