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*   Baseline Correction and Noise Elimination
Baseline correction and noise elimination algorithms analyze ion profiles (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 specified retention time range.
Note  In contrast to thresholding, which processes each scan independently while ignoring the previous or following scans, the Baseline Correction and Noise Elimination feature processes data in a chromatographic time domain, following trends over a specified retention time range.
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To apply baseline correction and noise elimination to your data
1.
Click the Chromatogram Processing Utilities button, , and choose Baseline.
The Baseline & Noise dialog box opens. See Baseline & Noise dialog box.
2.
3.
Click Calculate.
4.
Baseline & Noise dialog box
Specifies the mass difference within which the algorithm merges spectral peaks into one m/z value. A low value might result in more components (oscillating ions) and a high value can result in fewer components (merging ions).
Processes only spectra in MS1 stage (full scan).
Divides the chromatogram 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. Avoid segmentation if you use a LOESS derivative filter or if results obtained without segmentation are acceptable.
Applies one of the following methods to your chromatogram: Top-Hat filter, Savitzky-Golay derivative filter, or LOESS derivative filter.
A morphological two-step filter. First, the algorithm searches the average value (opening) of signal on an area around the analyzed peak and then it subtracts this value from the original analyzed peak.
Savitzky-Golay Derivative Filter
Baseline is defined by the point where the first derivation of a smoothed ion profile (values from Savitzky-Golay filter) is smaller than the value represented by the parameter Power. This baseline is then subtracted from the original ion profile. Time domain is determined by the Length parameter.
Principally identical with the Savitzky-Golay derivative filter but it does not require equidistant sampling.
Applies the following methods individually or simultaneously: Counter filter reduces chemical noise and Quantile filter reduces electronic noise.
Counts the occurrence of non-zero peaks in ion profile. If the percentage of signal occurrence is higher than the Length parameter, the ion is considered as chemical noise and the whole ion profile is removed.
Counts the occurrence of non-zero peaks in neighboring space on both sides (2×Length + 1 peaks). If the percentage of signal occurrence is smaller than the Fraction parameter, the analyzed peak is removed. This filter removes narrow peaks.
Resets the chromatogram to its original (before baseline correction and noise elimination) state.
Opens the Save Baseline & Noise Parameters File dialog box where you save your current parameters to a threshold parameters file (.baseline.par).
Opens the Open Baseline & Noise Parameters File dialog box where you can choose a threshold parameters file (.baseline.par) to load.
 
Baseline & Noise wizard dialog box
Specifies the mass difference within which the algorithm merges spectral peaks into one m/z value. A low (Soft) value might result in more components (oscillating ions) and a high (Strong) value can result in fewer components (merging ions).
Processes only spectra in MS1 stage (full scan).
Applies the methods specified in the detailed Baseline & Noise dialog box: Counter filter reduces chemical noise and Quantile filter reduces electronic noise.
Resets the chromatogram to its original (before baseline correction and noise elimination) state.
Opens the Save Baseline & Noise Parameters File dialog box where you save your current parameters to a threshold parameters file (.baseline.par).
Opens the Open Baseline & Noise Parameters File dialog box where you can choose a threshold parameters file (.baseline.par) to load.


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Related Topics:
  Fragment Ion Search (FISh)
  Force Mass Tolerance
  Matrix Conversion
  Thresholding
  Smoothing
  Base Peak Chromatogram
  Background Subtraction
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