Install and startupWindows computersMac computers (OS X)Linux computersStarting Chrombox C from the Matlab desktop (on all systems)Changing settingsUpdatingTutorial 1 - Basic functions1.1. Startup and select method1.2. Importing chromatograms:1.3. Retention index calibration1.4. Integration and identification1.5. Editing peaks1.6. Quantification and reportingKeyboard shortcutsScaling / scrollingSelectionIntegrationAdd and identify peaksLocking and unlockingLabels and plotting

The following text styling is applied in this document. Commands, paths or filenames are denoted by: command, or path\filename.ext. Buttons in the graphical user interface are shown as [Button]. Keys on the keyboard are denoted by [Key]. A parameter to be set is denoted by parameter, and a value of a parameter or an option in a menu is denoted by option.

Install and startup

Quick start

Windows computers

If installed on a server you may have to use one of the methods described below:

An example of cstart.m is shown below:

You can also create a desktop shortcut by copying the shortcut to Matlab and adding the following to the destination /automation /r cstart An example of how it can look is shown below:

C:\MATLAB6p5\bin\win32\matlab.exe /automation /r cstart

Mac computers (OS X)

As an alternative to the above procedure, Chrombox C can be started by the following method:

An example of cstart.m is shown below:

Linux computers

As an alternative to the above procedure you can also start Chrombox C by cstart.m as described for Mac computers above.

Starting Chrombox C from the Matlab desktop (on all systems)

On all operating systems you can use the following procedure to start Chrombox C.

In a minimized Matlab session (running in terminal without Matlab desktop) you can use the cd command to set the working directory and run cc_startscript to start the program.

Changing settings


The part to edit in cc_localsettings.sdv is between the two semicolons in the line shown below.

Alternatively, you may select the new code by the following procedure:

Tutorial 1 - Basic functions

The main purpose of this tutorial is to get used to basic functions in the program, how to use retention indices for identification, and basics of quantification and reporting. Fatty acid methyl esters (FAME) in two samples of marine algae will be identified and quantified using a predefined template.

1.1. Startup and select method

Figure 1.1. Main window at startup

1.2. Importing chromatograms:

Figure 1.2. The Import Box window after the files have been loaded

1.3. Retention index calibration

Identifications in this tutorial are based on the use of retention indices. Since the analytes are fatty acid methyl esters (FAME), the retention index scale is Equivalent Chain Lengths (ECL) where the ECL value for a saturated compound by definition is equal to the number of carbons in the fatty acid chain.

The chromatogram in the main window should now show peaks that have integer retention indices. You can also verify the retention index by clicking on a peak and inspect the information box.

Figure 1.3. The window for calibrating retention indices

1.4. Integration and identification

1.5. Editing peaks

You can edit areas and identifications in the chromatogram. An example for the area around the 18:1-monoenes is shown in figure 1.4. The peak to the left is identified as 16:4 n-1. However, it has a shoulder, and the template says that the shoulder should be 18:1 n-9. You can correct this by the following procedure:

Figure 1.4. The 18:1 area in Sample “ALGAE 40” before (upper) and after (lower) editing

1.6. Quantification and reporting

When you have edited areas and identifications it is time for quantification of the samples.

The GLC793 sample is applied for calculation of response factors and contains equal amounts of common fatty acids. Before you can quantify the peaks you must ensure that this sample has correct identifications. It should contain the following fatty acids: 12:0, 14:0, 14:1 n-5, 15:0, 16:0, 16:1 n-7, 17:0, 17:1 n-7, 18:0, 18:1 n-9, 18:2 n-6, 18:3 n-3, 18:3 n-6, 20:0, 20:1 n-9, 20:2 n-6, 20:3 n-3, 20:3 n-6, 20:4 n-6, 20:5 n-3, 22:0, 22:1 n-9, 22:4 n-6, 22:5 n-3, 22:6 n-3, 24:0 and 24:1 n-9. It is possible that 20:0 is identified as 18:4 n-3 since these two peaks has almost identical retention indices.

The reports are generated according to the template. Unidentified peaks are summarized and reported as “other”. In most cases, the fields of interest are adjusted area percents and amounts. The amounts are calculated according to the internal standard. The amounts of the internal standard are specified in the method settings, but the amounts can also be edited in the “IS Amt.” field in the main window.

Note that the reported area percent, adjusted area percent and the amount of the internal standard (23:0) is zero, even though it is present in the sample. This is because the internal standard is added, and not originally present in the sample.

The amounts are in this case μg FAME present in the samples. Selected fields for “ALGAE 40” are presented in Table 1.1.

Table 1.1. Results for sample "ALGAE 40"

Keyboard shortcuts

Scaling / scrolling



Add and identify peaks

Locking and unlocking

Labels and plotting