Greetings. Our lab has a Perkin-Elmer Clarus 500 GC equipped with an autosampler and an electron capture detector (ECD). We run the instrument using the TotalChrom software (also called TCNav). When we run samples, the instrument is supposed to save two types of output files: .raw files and .rst files. The .raw files are just the raw chromatograms. The .rst files are processed chromatograms where the peak areas have been integrated and reported. However, all of our .rst files are 0 kb files with no data in them. Hence, we don't know any of the areas of any of our peaks! Has anybody encountered (and solved) this problem? Why isn't the software calculating and/or storing my peak areas in the .rst files? Thanks!
Hello. Sounds to me that you are setting up your report, sequence, or processing wrong. Unlike the PE series 200 HPLC system, the GC doesn't use link boxes/modems and I don't remember us doing much to have the data saved.
Additionally, what makes me believe something in those above is wrong is that with TotalChrom you don't need to process your data to see your peak areas, raw files have that. You only need to process to see system suit parameters (tailing factor, k', resolution, etc) and for compliance with regulatory organs for industry people.
This is a very brief overview of how I used to set it up:
1) Create Method:
- Choose Channel for data collection in Data Acquisition. Channel A is for headspace and Channel B is for liquid injection.
- Set up your critical parameters (flow, pressure, oven temp, etc).
- Integration parameters can be adjusted later after injections are done.
- File, Save As, name. Don't use too long names and don't add spaces in the title as sometimes this causes the file to corrupt when processing. Use for example "Product-Assay-Initial-Date".
2) Create Report:
- Go to Report Format on main menu.
- Type in title, header, footer.
- Remove all parameters you don't want to report such as %Peak Area, Adjusted Amount and leave the things you need (Peak Area, Peak Height, etc).
- Edit -> Components and you can add other things to report such as Internal Standard ratio.
- Go to Options, and make sure the box for Print Report With Replot is checked. This will include the chromatogram in your processed data. Otherwise, once you process it will just print text without the chromatograms.
- File, Save As, name.
3) Create Sequence:
- Once you open Sequence from the main menu a window will pop up (Global Parameters). Make sure the right instrument is selected. Also choose Build From Template. Click OK.
- Next menu is Sequence Template. Make sure you load both channels fields with the method you created. However, load the channel you are collecting data from first. So if you are doing headspace, load Channel A first and select your method; then load Channel B and select the same method.
- In the actual sequence injection builder, work on Channel A sheet when running headspace and on Channel B when running liquid injection (they are sometimes hidden in the lower left corner). Build your injections and rows.
- In the columns Method and Report make sure you select the method and report you created above. If those are hidden, right click on any column and go to Hide/Unhide to show them.
- File, Save As, name.
4) Setup:
- Go to Setup on the main menu. Now, some software is set up with only the option to load a sequence. Some have option for quick start, load method, and load sequence. You need to go to Sequence and load the one you made above.
- Check the box for Suppress Processing otherwise it will automatically process each injection without you reviewing and adjusting integration parameters.
5) Run:
- Go to Run and start your sequence. Headspace needs to be started from the unit itself.
6) Data Analysis:
- At this point you should be able to review your injections including peak areas.
- Open Graphic Editor from the main menu. Find your injection name and open it.These are your raw files.
- It should load your peaks and integration parameters because the sequence had the method and report linked to it. If you have problems or need to load different methods, do so from File ->Method/Report.
- Adjust your integration parameters from the tool options above.
- Save Integration.
Now you have everything you may need to academic studies but if you want to process:
7) Process:
- Go to Batch from main menu.
- Load your sequence and report methods.
- Select the correct channels, A or B depending on what you ran.
- In Start Analysis choose Peak Detection; in End Analysis: Post Analysis Detection (but Replot Generation may work); Batch Execution is Interactive; Batch Plotter is Sequence Printer.
- In Raw File Treatment choose Use Existing Raw File.
You can go to Review from the main menu to review the final processed data and sign it electronically or you can go to Summary and create a template to report your summarized peak areas and results (if you type in formulas). From main menu -> Apps (tool line) -> System Suit you can choose the standard injections to have the system report your system suitability parameters.
Petroslav, thanks for your very detailed response. Our method and our sequence both work fine, that is no problem. We are using the autosampler and injecting the samples into our B injector port, which is connected to an Electron Capture Detector on our instrument. All of that is fine -- the method works, the sequence works. And the raw chromatograms all look fine, we are getting nice peaks, etc. But we are only getting .raw output files, not .rst output files, and the software is not integrating the peaks or reporting peak areas. We will go through your answer in more detail to see if it gives us some clues as to what we have done wrong. Thanks again for taking the time to write a very detailed reply.
- Badges
- Science topic
- Similar topics
- Instrumentation Engineering
- Instruments