Integration
Analyze → Integrate finds peaks on the chromatograms extracted by Get signals. The channel’s integrator does the detection. The default integrator name is Quanto.
What the Quanto integrator does
It smooths when the channel’s Savitzky–Golay length and order are both on, then looks for peaks and builds a baseline under each one. The baseline types it assigns are:
- Flat — a level baseline.
- Left and Right — the baseline is dropped from one side.
- V to V — valley to valley, between two peaks.
- Trend line — a sloping baseline along the local trend.
- Zero — baseline at zero.
You do not pick “drop”, “valley”, or “tangent skim” as separate menu items. Those shapes come out of the integrator settings on the channel (Integrator settings, key=value text). The baseline modes exposed for that integrator are fixed, lowest point between the offsets, and lowest point between the baseline offsets. Expected retention time is passed in for that integration call and is not written back onto the channel.
The peak’s response is the area, unless the analyte has Quantitate by height turned on, in which case the response is the height. Qualifier ratios use that same response. See Qualifiers.
Retention-time window and which peak is kept
The analyte’s expected RT and time window do not create the peak. They choose which integrated peak is the analyte. See Peak identification.
Manual integration
Drag a new baseline on the chromatogram to replace the automatic peak. The manual peak is stored separately from the original automatic peak. Reports can read Peak.Area (the current peak), Peak.AutoInt.Area (the original), and Peak.ManInt.Area (manual only; blank when you have not integrated by hand).
Analyze → Reset manual integration clears manual peaks for the entire batch, the selected samples, or the selected analytes.
Edit → Undo can undo a manual integration as a review action.
Thresholds
Peaks under the effective threshold are dropped and the integration is left without them. Calibration and QC samples always use threshold 0, so their peaks are not removed by this cutoff.
Threshold absolute
On the channel, Threshold absolute. When this number is set, it wins over the percent mode. Empty means “use the percent mode, or no cutoff”.
Threshold percent and dose
On the quant, Threshold % of dose response (default 0, which means that quant imposes no cutoff) and Threshold dose. An empty dose name means the lowest calibration dose. The cutoff is that percent of the response at that dose. If several quants share the channel, the lowest of those percent cutoffs is used.
Effective threshold
Threshold (effective) is the cutoff actually applied: the absolute value when it is set, otherwise the percent result. Threshold source names which one was used (“Threshold absolute”, the quant and dose, “No threshold…”, or “Calibration and QC samples use threshold 0.”).
The chart can draw this line. In grid configuration, field appearance has Threshold (effective) and Ignore threshold zoom.
Signal-to-noise and minimum peak width
The integration path does not expose a user setting named signal-to-noise or minimum peak width for routine peak detection. Signal-to-noise appears on deconvoluted components (default minimum 3 in the deconvolution engine). Peak width is a measured result (width at half height), not a rejection threshold you type in. See SCAN deconvolution.
Set the absolute threshold or the percent-of-dose threshold when you need to ignore noise peaks. Set Savitzky–Golay when you need to smooth before those peaks are found. See Smoothing.