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####Methods

1. File Conversion
2. Baseline Correction
3. Curve Fitting

####File Conversion

Use the FileIO class to import data into the MATLAB workspace. Initialize the FileIO class with the following command:

obj = FileIO
```

Import files using the `import` method. For example, the following command will prompt you to select Agilent (.D) files to import into the MATLAB workspace:

````matlab
data = obj.import('FileType', '.D')

Append an existing data structure with additional files of any supported file type. Just include the name of your data structure when using the import method.

data = obj.import('FileType', '.D', 'Data', data)

####Baseline Correction

Use the BaselineCorrection class for baseline correction. Initialize the BaselineCorrection class with the command:

obj = BaselineCorrection

Calculate baselines with the baseline method. For example, determine the baseline for all ion chromatograms in your LC/MS dataset:

data = obj.baseline(data, 'Samples', 'all', 'Ions', 'all')

Refine the baseline calculation by adjusting the parameters Smoothness and Asymmetry. Typical values for Smoothness range from 1E3 to 1E9, and Asymmetry from 1E-1 to 1E-5.

data = obj.baseline(data, 'Samples', 'all', 'Ions', 'all', 'Smoothness', 10^7, 'Asymmetry', 10^-3)

####Peak Integration

Use the PeakProcessing class for peak detection and peak area determination. Initialize the PeakProcessing class with the following:

obj = PeakProcessing

Calculate peak area using the integrate method. Use the following command to automatically detect and integrate the largest peak in each ion chromatogram from your LC/MS dataset:

data = obj.integrate(data)

Find and integrate peaks within a given time frame. For example, find the largest peak in each ion chromatogram with a retention time between 10-20 min:

data = obj.integrate(data, 'WindowCenter', 15.0, 'WindowSize', 10.0)