Starting A Chromatographic Run

Some activities and maintenance procedures (e.g., pumping in isocratic mode, turning the detectors on and off) can be accomplished through the individual Method screens. But most operations (gradients, automatic runs with autosamplers, data collection, PAD) require that a programmed run be initiated.


First double-check the Method to make sure it is correct. In particular, check that the Detector Schedule has the correct detector conditions and run time, that the Pump Gradient Schedule has the correct solvent composition and flowrate, and that the Data Name and Data Collection Rate are satisfactory.

Next open the DATA ACQUISITION OPTIONS section of the Method:

Set the TRIGGER TYPE to Manual if you will be using a manual injector. If using an autosampler, set it to Automatic or External as appropriate (See the Autosampler section to determine which to use.)

Next enter the number of the first run, and the number of runs in the series (maximum = 999). Then click OK. The system is now ready to run.


Double-click on the RUN STATUS icon, which will open up the RUN STATUS box:

Click EQUIL to send the information from the Method to the epsilon system. EQUIL puts the conditions in each Method module into effect. Where there are time lines, as in the Detector Schedule, it puts the 0.0 time line into effect. Note that the EQUIL function here is just a formality to ensure that the starting conditions from the Method are in effect -- the system should have been equilibrating for several hours before serious data collection is attempted.

To begin the series of runs, click RUN. The run will start within a few seconds if an automatic or manual trigger has been selected. If an external trigger has been selected, the run will await a signal from the autosampler . When the run starts, a graph will appear showing the chromatogram in real time:

The EQUIL and RUN functions in the RUN STATUS box will be unavailable, and the PAUSE, END and ABORT buttons will become available.

PAUSE stops the timers from all modules. Thus, the current gradient conditions at any time during the run can be held constant. This feature can be used during method development, for example, to hold the gradient constant while peaks elute. A CONTinue button appears when PAUSE is pressed, allowing resumption of the run.

END stops data collection and saves the data to disk. END does not end the pump's run, in case there is a gradient or column wash programmed in. If you've ENDed the data and are sure you want to terminate the pump's run, press ABORT to terminate the run.

ABORT cancels all timed events and returns the system to 0.0 time conditions.

Several events occur onscreen while the run is in progress. Data and messages will scroll upwards on the output screen, which appears in the background. Superimposed on this output screen are the graph, which shows a chart-recorder style image of the detector output, and the RUN STATUS box. In addition to the pushbuttons described above, the RUN STATUS box displays the elapsed time and messages.

The listing and graphing of data during the run are turned on and off by options in the CONTROL MENU:

Graph colors are selected in the GRAPHICS MENU. The graphics capabilities of ChromGraph Control are not as extensive as those of ChromGraph Report, but the Zoom Cursor, Overview Window, and Grid Dots are available.

When the first run is complete, the system prepares for the next run in the series. The instruments return to time 0.0 conditions. The data are saved, the RUN NUMBER is incremented by one, the NUMBER OF RUNS is decremented by one, and the new run is either started or waits for a trigger.


Additional runs may be scheduled while a batch of runs is in progress. Simply open the STATUS menu and take the CHANGE NUMBER OF RUNS option:

Then enter the updated LAST RUN NUMBER.


If you've started a bunch of runs and need to check that everything in the Method is correct, you can do this without stopping the runs. Take the REVIEW METHOD option under the STATUS menu:

A copy of the Method will appear in the output window, and you can review it there. For this to occur, the scrolling of data on the output window must stop (no data points are lost, however). To turn data scrolling back on, take the LIST RUN DATA option under the CONTROL menu.


Several files are saved to the default data location in conjunction with a programmed run. These are:

DATA FILES contain the collected digitized data from the detectors. These have the format NAME###X.DAT. NAME is the data name, any combination of spaces and characters, ending in a letter. ### is the run number from 1-999. X is the detector code, from A-D, corresponding to detectors 1-4. Each detector will produce its own data file. The extension ".DAT" stands for data, and will automatically be appended.

Data names can theoretically be up to 127 characters long, including the path (thus, C:\BAS2\DATA\mydata002A.dat = 27 characters). Some advanced procedures may require shorter names, so we recommend using names with total lengths (including the path) of less than 33 characters.

For display purposes, a filename may be truncated somewhat in various places in the program.

LOG FILES have the Method name, followed by a ".LOG" extension. They record the runs made under each method. Log files are created automatically whenever you run a Method. They can be found in the startup directory (usually C:\BAS2 or C:\BAS3) and viewed with any text editor or word processor. When a log file reaches 100 KB it is automatically cleared, and its contents transfered into a backup file with the same name and a ".LOK" extension.

BACKUP METHOD FILES are copies of the Method that are associated with data files for future reference. If you made runs 1-20 from the Method MCAT.MTH, for example, you would find the following files in your default data location:

  • MCAT.MTH (current Method file)
  • MCAT.LOG (log file)
  • MCAT001A.DAT through MCAT020A.DAT (20 data files)
  • MCAT001A.MTH (Backup Method File)

The last file is a copy of MCAT.MTH. Because of its hybrid name (DATA name + .MTH) it will not normally be used as a Method file, and thus will never be modified. It serves as a record of the conditions under which the runs were made, and thus should not be altered.

Only one Backup Method File will be made for any sequence of runs. However, if you start runs individually, one by one, a Backup Method will be made for each. To turn off the backup feature, click off the Auto-Backup .MTH feature under Setup Options.

A complete list of all file types used by ChromGraph Control and ChromGraph Report is available here.