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Example 2: Raw data processing

Goal: You want to find all peaks in your raw data.

The first step shown here is the elimination of noise using the NoiseFilter. The now smoothed raw data can be further processed by subtracting the baseline with the BaselineFilter. Then use the PeakPicker to find all peaks in the baseline-reduced raw data.

TOPP_raw_data.png

We offer two different smoothing filters: a Gaussian filter and a Savitzky Golay filter, which can be selected by the option 'type'. If you want to use the Savitzky Golay filter, or our BaselineFilter with non equally spaced raw data, e.g. TOF data, you have to generate equally spaced data by setting the 'resampling' option.

Finding the right parameters for the NoiseFilter, the BaselineFilter and the PeakPicker

Finding the right parameters is not trivial. The default parameters will not work on most datasets. In order to find good parameters, we propose the following procedure:
  1. Load the data in TOPPView
  2. Extract a single scan from the middle of the HPLC gradient (Right click on scan)
  3. Experiment with the parameters until you have found the proper settings

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