public static udtSICPeakFinderOptionsType GetDefaultSICPeakFinderOptions()
{
var peakFinderOptions = new udtSICPeakFinderOptionsType
{
IntensityThresholdFractionMax = 0.01f, // 1% of the peak maximum
IntensityThresholdAbsoluteMinimum = 0,
SICBaselineNoiseOptions = NoiseLevelAnalyzer.GetDefaultNoiseThresholdOptions()
};
// Customize a few values
peakFinderOptions.SICBaselineNoiseOptions.BaselineNoiseMode = NoiseLevelAnalyzer.eNoiseThresholdModes.TrimmedMedianByAbundance;
peakFinderOptions.MaxDistanceScansNoOverlap = 0;
peakFinderOptions.MaxAllowedUpwardSpikeFractionMax = 0.2f; // 20%
peakFinderOptions.InitialPeakWidthScansScaler = 1;
peakFinderOptions.InitialPeakWidthScansMaximum = 30;
peakFinderOptions.FindPeaksOnSmoothedData = true;
peakFinderOptions.SmoothDataRegardlessOfMinimumPeakWidth = true;
// If this is true, will ignore UseSavitzkyGolaySmooth
peakFinderOptions.UseButterworthSmooth = true;
peakFinderOptions.ButterworthSamplingFrequency = 0.25f;
peakFinderOptions.ButterworthSamplingFrequencyDoubledForSIMData = true;
peakFinderOptions.UseSavitzkyGolaySmooth = false;
// Moving average filter if 0, Savitzky Golay filter if 2, 4, 6, etc.
peakFinderOptions.SavitzkyGolayFilterOrder = 0;
// Set the default Mass Spectra noise threshold options
peakFinderOptions.MassSpectraNoiseThresholdOptions = NoiseLevelAnalyzer.GetDefaultNoiseThresholdOptions();
// Customize a few values
peakFinderOptions.MassSpectraNoiseThresholdOptions.BaselineNoiseMode = NoiseLevelAnalyzer.eNoiseThresholdModes.TrimmedMedianByAbundance;
peakFinderOptions.MassSpectraNoiseThresholdOptions.TrimmedMeanFractionLowIntensityDataToAverage = 0.5f;
peakFinderOptions.MassSpectraNoiseThresholdOptions.MinimumSignalToNoiseRatio = 2;
peakFinderOptions.SelectedIonMonitoringDataIsPresent = false;
peakFinderOptions.ReturnClosestPeak = true;
return(peakFinderOptions);
}
