Proteomics-MSBaseline - Softberry Mass Spectra (SMS) processing tools. Baseline detection and subtraction.
This step of data processing is applied for elimination of the systematic artifacts that occur due
to matrix and chemicals used in the experiments or as a result of detector overload. It results in
background noise that may occur to be significant for some m values. The initial step in background
noise removal is identification of peaks (local signal maxima that are located far enough from each other).
The distance between peaks is determined by the 'Baseline parameter' value (default= 0.005). This parameter
defines the minimal m distance, over which the two neighboring peaks 1 and 2 are to be located in the way, when:
After peaks identification, algorithm detects the points with signal minima located in intervals between peaks. These are the base points for calculation of background noise line. Over base points the baseline for all spectrum points is built by interpolation. In case when in some spectrum parts the value of base signal exceeds the original one, the new base points selection from neighboring ones occurs.
The values of base signal intensity are subtracted from the original one. At that, if value of original signal has occurred below zero, it is equated to zero. The result of background subtraction is shown in figure 1.
Input: m/z - Intensity data
#M/Z,Intensity -7.8602611e-005,4.1126194 2.1773576e-007,4.0764203 9.6021472e-005,4.0040221 0.00036601382,4.1186526 0.00081019477,4.0040221 0.0014285643,3.9617898 .... 19742.941,4.077895 19745.564,4.0772248 19748.187,4.0772248
Figure 2. Example file with mass spectra data in CSV format.
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