Baseline correction and noise elimination algorithms analyze ion profiles (selected ion chromatograms) of all ions appearing in spectra over the entire region of a chromatogram. In contrast to thresholding, where the individual scans and their spectral peaks are independently analyzed and modified, baseline correction and noise elimination analyze and modify spectral peaks in a given retention time range.

To apply baseline correction and noise elimination to your data, click on the Chromatogram Processing button and choose the Baseline pop-up menu item. The dialog window will appear with the following parameters:

Process Top Stages Only: If checked, spectra in MS1 stage (full scan) will be processed.

Segmentation: If checked, the chromatogram will be divided into discrete parts to which the algorithms are applied separately. This option can provide better results if a chromatogram exhibits diverse shape, peak density and baseline characteristics over the retention time scale. Segmentation should be avoided if a Loess derivative filter is used.

Use Baseline Correction: If checked, one of the following methods will be applied to your chromatogram: Top-Hat filter, Savitzky-Golay derivative filter, or Loess derivative filter.

Use Noise Elimination: If checked, the following methods can be applied individually or simultaneously: Counter filter to reduce chemical noise and Quantile filter to reduce electronic noise.

Smoothing is a process by which ion profiles (not total ion chromatogram) for every ion (m/z value) found in the data file are averaged with their neighbors in a time series. Smoothing can increase correct component detection and can eliminate “spikes”, which cause false positive results.

To apply smoothing to your data, click on the Chromatogram Processing button and choose the Smoothing pop-up menu item. The dialog window will appear with the following parameters:

Smooth Top Stages only: If checked, smoothing will only be applied to MS1 stage (full scan).

Segmentation: If checked, the chromatogram will be divided into discrete parts to which the algorithms will be applied separately. This option can provide better results if the chromatogram exhibits diverse shape, peak density and baseline characteristic the retention time scale.

Method: This group box includes the following smoothing methods: Savitzky-Golay, Median and Loess. In contrast to Median and Loess methods, the Savitzky-Golay method requires time-equidistant scans.

To eliminate the background signal from an active scan, or from the average of spectral scans, a manual background subtraction can be carried out. Mass Frontier allows you to set the location of two representative background scans by pressing the Manual Background Subtraction button and then left-clicking the scan point in the chromatogram pane. The background scans are indicated by a vertical line, which is depicted in a different color (by default green) from the scan line. The resulting spectrum will be displayed in the Scan tab. To cancel a background subtraction, press the Cancel Background Subtraction button. The Selected Ion Chromatogram feature can help you to choose the two most representative background scans. Such background scans can be used in Manual background subtraction option in Automated Components Detection and Spectra Deconvolution procedures.

If you would like to see the effects of the background subtraction on a scan, you can copy both the extracted and original spectra to Database Manager and compare them using the spectra comparison routine in the Compare Spectra tab.

Background subtraction can be used in conjunction with Selected Ion Chromatogram feature. In this case the SIC profiles are extracted from background subtracted scans.

Mass Frontier enables you to display a chromatogram for a selected ion in a different color. The selected ion chromatogram (SIC) is sometimes called an individual or single ion chromatogram, ion profile. The program can display up to three selected ion chromatograms per window.

To display an SIC for a particular mass-to-charge ratio:

• Click on the spectral peak of interest on the Scan page

• Or, select the Data tab and click the m/z value in the mass-to-charge ratio table

• Or, click the Selected Ion Chromatogram button

In either case a dialog window will appear in which you can change or add the mass-to-charge ratio and confirm your choice. This dialog window allows you to select a color for a particular m/z value.

Mass Frontier extracts the SIC from the original file, and this process can be time-consuming for chromatograms with a large number of scans. However, because Mass Frontier is a multithreading application, you can still use other windows during the SIC extraction.

A selected ion chromatogram is very useful feature for verifying automated component detection and spectra deconvolution results. An SIC helps you to quickly recognize mixture components in a peak region. An SIC of model peaks should be examined for any component you may wish to use in further analysis. Remember that some structural (alkanes) or optical isomers produce almost identical mass spectra and even if you can clearly see two or more maxima in a peak region, an SIC may not reveal a multi-component profile.

An SIC can help you to determine whether or not the composition of the background changes over the course of a run. To view the background profile, extract the SIC of a base peak, or prominent peak, from a scan which is clearly in a non-peak region. If the SIC of a background peak has a variable profile around the peak you are focusing on, choose two scans with different SIC profiles for background subtraction.

Background subtraction can be used in conjunction with SIC option. In this case the SIC profiles are extracted from background subtracted scans.