Preprocess data

This operation preprocesses one or more Raw Data elements, applying the selected methods to each spectra. If you apply peak detection, this operation returns one or more Peak List elements. Otherwise, it returns one or more Raw Data elements.

Usage

You can execute this operation by clicking the button or following the menu Preprocess/Preprocess data.

A dialog will appear allowing you to select the following options:

• Raw Data: previously loaded Raw Data.
• Intensity transformation (scaling) method: None (not apply), Logaritmic, Logaritmic with base 10, Logaritmic with base 2 or Square root.
• Smoothing method: None (not apply), moving average window (MALDIquant) or Savitzky Golay (MALDIquant).
• Baseline correction method: None (not apply), Top Hat, Snip, Median or Convex Hull (all from MALDIquant).
• Standardization method: None (not apply), total ion current (TIC), Probabilistic Quotient Normalization (PQN) or median (all from MALDIquant).
• Peak detection method: None (not apply), MassSpecWavelet or MALDIquant.
  
  • If you choose "None", no peak detection will be performed. However, you can choose whether you want to convert the input data into a peak list (which can be useful if peak detection has been already applied to the input raw data) or not.
  • If you choose "MassSpecWavelet", you also have to set:
    • Signal to noise ratio: SNR threshold used to identify peaks. Default is 6.
    • Peak scale range: The CWT scale range of the peak. Default is 2.
    • Amplitude threshold: The minimum peak amplitude. Default is 0.0001.
  • If you choose "MALDIquant", you also have to set:
    • Signal to noise ratio: SNR threshold used to identify peaks. Default is 3.
    • Half window size: The resulting window reaches from mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]. A local maximum have to be the highest one in the given window to be recognized as peak. Default is 60.
• Minimum peak intensity: a non-negative number indicating the minimum peak intensity to filter out peaks. Peaks with an intensity lower than this threshold are discarded.
• Keep original data: if you select this option, original data is maintained in the cilpboard. Otherwhise (by default), original data is removed.