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Chromatography Toolbox (v0.1.51) provides command line data processing methods for chromatography and mass spectrometry data in MATLAB.

Table of Contents

1. Initialize
2. Import
3. Baseline
4. Smooth
5. Integrate
6. Visualize

Initialize

Initialize the Chromatography class to use any of the following methods: import, centroid, baseline, smooth, integrate, visualize.

obj = Chromatography

Import

Import raw data into the MATLAB workspace with the import function. Supported file formats include: Agilent (.D), Thermo (.RAW), and netCDF (.CDF).

data = obj.import(filetype, 'OptionName', optionvalue)

Examples

% Import Agilent '.D' files
data = obj.import('.D');

% Import NetCDF '.CDF' files and append data to an existing data structure
data = obj.import('.CDF', 'append', data);

% Import Thermo '.RAW' files without status updates in the command window
data = obj.import('.RAW', 'progress', 'off');

Baseline

Perform baseline correction with the baseline function.

data = obj.baseline(data, 'OptionName', optionvalue)

Examples

% Get baselines for all total ion chromatograms (TIC), for all samples
data = obj.baseline(data,...
    'samples', 'all',...
    'ions', 'tic',...
    'smoothness', 1E7,...
    'asymmetry', 1E-5);

% Get baselines for all extracted ion chromatograms (XIC), for samples #2 and #5
data = obj.baseline(data,...
    'samples', [2,5],...
    'ions', 'all',...
    'smoothness', 1E6,...
    'asymmetry', 5E-6);

% Get baselines for selected extracted ion chromatograms (XIC), for all samples
data = obj.baseline(data,...
    'samples', 'all',...
    'ions', [1:10, 23, 27, 80:150]);

Smooth

Smooth raw data with the smooth function.

data = obj.smooth(data, 'OptionName', optionvalue)

Examples

% Smooth all total ion chromatogram (TIC), for all samples
data = obj.smooth(data,...
    'samples', 'all',...
    'ions', 'tic',...
    'smoothness', 1000,...
    'asymmetry', 0.5);

% Smooth all extracted ion chromatograms (XIC), for samples #1-3 and #6
data = obj.smooth(data,...
    'samples', [1:3,6],...
    'ions', 'all',...
    'smoothness', 10,...
    'asymmetry', 0.5);

% Smooth selected extracted ion chromatograms (XIC), for samples #2, #4, and #6
data = obj.smooth(data,...
    'samples', [2,4,6],...
    'ions', [1:100, 150:250, 300, 400],...
    'smoothness', 500,...
    'asymmetry', 0.5);

Integrate

Find peaks and determine peak area using the integrate function.

data = obj.integrate(data, 'OptionName', optionvalue)

Examples

% Find and integrate the largest peak between 19.5 and 21.5 minutes in the total ion chromatogram (TIC), for all samples
data = obj.integrate(data,...
    'samples', 'all',...
    'ions', 'tic',...
    'center', 20.5,
    'width', 1.0);

% Find and integrate the largest peak between 0 and 30 minutes in the total ion chromatogram (TIC), for samples #2-4 and #6
data = obj.integrate(data,...
    'samples', [2:4,6],...
    'ions', 'tic',...
    'center', 15.0,
    'width', 15.0);

% Find and integrate any peaks at 19.36 minutes for all extracted ion chromatograms (XIC), for all samples
data = obj.integrate(data,...
    'samples', 'all',...
    'ions', 'all',...
    'center', 19.36,
    'width', 0.01);

% Re-run the previous example, but reset/clear all existing peak data first
data = obj.integrate(data,...
    'samples', 'all',...
    'ions', 'all',...
    'center', 19.36,
    'width', 0.01,...
    'results', 'reset');

% Find and integrate peaks at 19.50 minutes and replace the results from the previous example
data = obj.integrate(data,...
    'samples', 'all',...
    'ions', 'all',...
    'center', 19.50,
    'width', 0.01,...
    'results', 'replace');

Visualize

Plot data and export high quality figures using the visualize function.

fig = obj.visualize(data, 'OptionName', optionvalue)

Examples

% Plot the total ion chromatograms (TIC) for all samples in a stacked layout using separate scales and show legend
fig = obj.visualize(data,...
    'samples', 'all',...
    'ions', 'tic',...
    'layout', 'stacked',...
    'scale', 'normalized',...
    'legend', 'on');

% Re-run the previous example, change the color to 'black' and save figure to a .PNG file with a DPI of 300
fig = obj.visualize(data,...
    'samples', 'all',...
    'ions', 'tic',...
    'layout', 'stacked',...
    'scale', 'normalized',...
    'legend', 'on',...
    'color', 'black',...
    'export', {'MyFileName', '-dpng', '-r300'});

% Plot selected XIC for all samples and overlay all chromatograms on the same scale between 10-30 minutes
fig = obj.visualize(data,...
    'samples', 'all',...
    'ions', [2,50],...
    'layout', 'overlaid',...
    'scale', 'full',...
    'legend', 'on',...
    'colormap', 'jet',...
    'xlim', [10,30]);

% Plot a single XIC for samples #1-2, and #5-6 in a stacked layout with separate scales and save figure to .JPG file
fig = obj.visualize(data,...
    'samples', [1:2,5:6],...
    'ions', 34,...
    'layout', 'stacked',...
    'scale', 'normalized',...
    'legend', 'on',...
    'colormap', 'hsv',...
    'xlim', [15,45],...
    'export', {'MyFileName2', '-djpeg', '-r400'});