Smoothing

Savitzky–Golay smoothing replaces each chromatogram point with a value from a local polynomial. The peak keeps its position better than a simple moving average. Quanto applies it to the extracted chromatogram before peaks are detected, so areas, heights, and concentrations use the smoothed trace.

A window of 0 or an order of 0 turns smoothing off. The raw points stay available; the trace that is integrated is the smoothed one when smoothing is on. The chromatogram shows the smoothed signal that was integrated.

Spectra in Compound Discovery use the same kind of smoother inside deconvolution (default window 9, order 5). That path is separate from the channel settings. See SCAN deconvolution.

Where to set it

On the channel, in Channels or Quant channels:

• SG length — odd number of points. 0 is off.
• SG order — polynomial order. 0 is off.

The column help says order 4 or 5 works best, and that the length should be the number of points across the peak at half height, typically 7–13. The length must be greater than the order when smoothing is on.

Propose SG width (method menu, or the channel toolbar) sets the length from the current sample. You still choose the order.

New channels start at order 5 and length 0, so smoothing is off until you set a length. SCIEX channels imported by that path are stored with both values at 0.

Limits

The spin offers lengths 0, then every odd length from 1 through 201, and orders 0 through 20. A larger odd length or a larger legal order that is already stored stays selectable.

If you set a length that is not above the order, the order is lowered to length minus one. If you set an order that is not below a positive length, the length moves up to the next odd count above the order. Length 0 leaves the stored order alone. Order 0 leaves the stored length alone.

Noise, height, and resolution

A wider window (or a lower order) removes more noise and also lowers the peak and can merge peaks that sit close together. A narrower window (or a higher order) keeps height and resolution and leaves more noise. Order 4 or 5 is the suggested starting point. Set the length from the peak width at half height, then look at the integrated peak before you rely on the area.