Subtracting Background Spectra

Mass Spectra usually have a higher noise level than UV spectra. Therefore, you may want to subtract the background spectra. (However, for UV channels, it is usually not necessary to change the default background subtraction.) There are two ways to subtract background spectra.

Peak Dependent Background Subtraction

Enable Background Subtraction on the context menu of the chromatogram. Return to the context menu and select Peak Dependent Ranges. Chromeleon automatically determines two ranges for calculating the background and then subtracts the entire mass or UV spectrum of these ranges. On the MS or UV tab page of the QNT Editor (see Data Representation and Reprocessing  The QNT Editor), define the number of mass spectra or UV spectra to be used for the two ranges. (For more information, refer to  Processing Mass Spectra and/or  Processing UV Spectra.)

Fixed Background Subtraction for the Entire Chromatogram

At the beginning of the chromatogram, hold down the right mouse button and select the baseline range for which the mass spectra (UV spectra) is subtracted. A context menu appears. Select Set Background Subtraction Range 1 to use the defined range as the first range for which to subtract the mass spectra (UV spectra) from the mass spectra (UV spectra) of the single peaks and/or from the retention time spectrum.

 Note:

Selecting Set Background Subtraction to Range 1 automatically enables the Fixed Background Ranges option of the Background Subtraction command on the context menu.

In the same way, select a baseline range at the end of the chromatogram. Select Set Background Subtraction Range 2 on the context menu to define this range as the second range for which mass spectra (UV spectra) is subtracted from the mass spectra (UV spectra) of the single peaks.

 Note:

It is useful, but not imperative, to define a second range; background subtraction can also be performed using only the mass spectra (UV spectra) of the first range.

The two defined ranges are marked by a horizontal line (in the same color as the spectrum, or in blue if no spectrum is available) and labeled "SB1" or "SB2" (SB = subtracted background). If the background subtraction range was used, the number of single mass spectra or UV spectra that were averaged is indicated in parentheses:

 Note:

It is possible to set the two ranges for background subtraction of mass spectra in a UV channel. However, Dionex recommends setting the two ranges in the corresponding MS channel because the respective peaks are visible only there.

Clear Background Subtraction Ranges removes the previously defined ranges.

Effects

The settings selected in the chromatogram are saved in the QNT File of the current sample. These settings overwrite the settings on the MS or UV tab page of the QNT Editor. It makes no difference whether background subtraction is defined on the Integration plot or in the QNT Editor. Thus, your input affects all samples that are evaluated using this QNT File.

 Tip:

Make sure that no peak of another sample is within the retention time used as the Background Subtraction Range in Fixed mode.

For a mass spectrum (UV spectrum) that was recorded between two ranges, the ranges are averaged and the result is subtracted. The mass spectra (UV spectra) of the two ranges are weighted based on the time distance from where the respective mass spectrum (UV spectrum) was recorded; that is, the range that is nearer to the respective mass spectrum (UV spectrum) is considered more.

If a mass spectrum (UV spectrum) is not located between the two ranges, only the averaged mass spectrum (UV spectrum) of the range next to the spectrum is subtracted.