Welcome to MSD ChemStation 101

Our technical service department receives quite a few MSD ChemStation software functionality related requests which are frequently forwarded to me. I’ve decided to start a blog series to address these requests. Feel free to leave requests in the comments if there’s something you need help with. I will primarily be working in the most current version of MSD ChemStation that I have: G1701EA.02.02, though I can offer help with AA.03, BA.00, and various DA and EA versions of the software.  Be forewarned; my experience is limited to Enviroquant and Enhanced ChemStation.

The first request I’m going to address is how to add or change  internal standard and surrogate compounds in a calibration using Enviroquant and Enhanced Chemstation, and how to configure the software to automatically calculate concentrations and surrogate percent recoveries using the internal standards. I will be using  the 524.3 list as an example. This technique is particularly useful if your lab is expanding the tests offered from hazardous waste (series 8000 methods) to waste water (series 600). Your compound lists and analytical columns will see little to no change, but your internal standard and surrogate compounds may be different. The technique is also useful if you are converting an external standard calibration to an internal standard calibration (for example, 8081) to avoid the closing calibration verification requirements.

Table 4 on page 35 of EPA Method 524.3 lists the target compounds, the internal standard compound each is associated with, and a recommended quant ion. The recommended column for this analysis is the 30m x 0.25mm x 1.4µm Rtx-VMS.

If you use these conditions, you should be able to match your compound list to the published elution order and retention times. The easiest way to reorganize the compound list is in Enhanced ChemStation  under the “Calibrate” menu. If your compound list does not contain the correct internal standards, or they are not configured as internal standards, you will need to use the Edit Compounds option found under the Calibrate menu in Enhanced ChemStation (or Initial Calibration menu in Enviroquant) to add them.

If you don’t have any configured internal standards, your quant database should look similar to the image above. If you have the wrong compounds configured as internal standards, delete them by right clicking on the compound and choosing the delete option. In order to add the first internal standard compound, right  click “Compound Database” at the top of the list, and chose the option “Insert ISTD Compound Below current Group” and then fill out the relevant information for the compound. Make sure you change the quant signal to “Target Ion” and use the recommended ion 114 (taken from EPA method 524.3 Table 4). Do the same for the other two internal standards. You’ll notice, however, that the internal standards are at the bottom of the compound list.

In Enhanced ChemStation, choose “Reorder Compounds” under the “Calibrate” menu, and a popup will open that allows you to move compounds by assigning them a new order number. You want to make sure you list all the compounds associated with internal standard  (IS) 1  before the compounds associated with IS 2, which should be listed before the compounds associated with IS 3. You will want to move the internal standard compounds above the compounds they are associated with. In the case of 524.3 on the Rtx-VMS, you will move 1,4-difluorobenzene above dichlorodifluoromethane, chlorobenzene-d5 between cis-1,3-dichloropropene and toluene, and 1,4-dichlorobenzene-d4 between isopropylbenzene and 4-bromofluorobenzene. I have not been able to find this functionality in Enviroquant.

At this point, if you were to calculate your results, you would see the Internal standards grouped above the target compounds, but we want to calculate the surrogate percent recoveries too.

To calculate the surrogate recoveries, the surrogates need to classified as such in the software. This is done by entering “S” in the edit compound type field under edit compounds on the “Identification” tab.

The expected spike amount for the surrogate and the control ranges are entered on the “Reporting” tab in Edit Compounds.


Now, when you calculate results, you should see the surrogate compounds grouped under the internal standard compounds with a calculation of the percent recovered.

I hope this first guide was helpful; don’t hesitate to add questions or suggestions in the comments below. Unless someone suggests something better, the next walk-through will be on running versions of MSD ChemStation that are incompatible with Windows 7 from the Virtual XP machine.



21 Responses to “Welcome to MSD ChemStation 101”

  1. Alan Sensue says:

    Great idea for a blog post Chris. I’m sure our customers will benefit.

    As you know, we (tech service) don’t have instrument software on our PC’s, so very seldom are we able to help our customers with their questions. Having you to help us out is much appreciated.

  2. Jason Hoisington says:

    This touches more on data acquisition than processing, but the E versions of MSD Chemstation can be picky about what version of Microsoft .NET framework are installed. E.02.01 requires Microsoft .NET 3.5, and I believe E.02.00 required .NET version 3.0. Having the wrong versions will generally cause communication issues with the instrument. If you’re not getting a complete system with computer from Agilent then this can trip you up during the setup process.

  3. Good point about the API issues, Jason. I believe the .NET differences in the versions of E.02 have to do with added compatibility for Windows Vista (E.02.01) and Windows 7 (E.02.02). Fortunately, you can run E.02.00 in the virtual Windows XP machine included with Windows 7. This is an easy way to sidestep OS compatibility issues as you upgrade your computers. This may be the subject for my next blog…

    While we are on the subject of Windows/ChemStation API issues, I want to point out that MSD ChemStation had problems with the transition from Microsoft’s .COM to .NET architecture. There are known issues with D.02 and the E versions prior to E.02. If anyone is running one these versions of the software and having productivity issues, they should contact Agilent. The HPIB 6890/5973 GC-MS combo requires D.03, while the LAN instruments should be upgraded to E.02.

  4. Mindy Froome says:

    I actually have a question on Chemstation Version D.02.00. I am loading it onto my computer and able to get the instrument to run but while it is connected to the network I am unable to connect to my local area network and the internet. Do you know if this is a glitch with the software or is there a way to set up the instrument so I am able to also access my local network. I have installed 2 network cards also. Do you have any suggestions. I had out computer guy look at it and so far cant figure it out.


  5. Mindy, I think I can help you over the phone. Email me your contact info. I’m currently out of the lab on a New England GC-MS seminar tour, but you should hear from me by Tuesday.

  6. Raj says:

    Hi Chris,
    I am using windows 7 with chemstation VERSION E.02.02 ..
    when I try to print custom report it crashes with following error..it was working fine with windows xp and version E.00.00
    Unfortunately, I have to update my computer with new version . Custom report doesn’t work with E.02.02
    do you have any idea how to fix this error ? .

    Problem signature:
    Problem Event Name: APPCRASH
    Application Name: msda.exe
    Application Version:
    Application Timestamp: 4dd245c9
    Fault Module Name: HiaCpCom.dll
    Fault Module Version:
    Fault Module Timestamp: 4dd23f9f
    Exception Code: c0000005
    Exception Offset: 0000390a
    OS Version: 6.1.7600.
    Locale ID: 1033
    Additional Information 1: 0a9e
    Additional Information 2: 0a9e372d3b4ad19135b953a78882e789
    Additional Information 3: 0a9e
    Additional Information 4: 0a9e372d3b4ad19135b953a78882e789

  7. Tingting says:

    Hi I am really excited to find this blog with tips and tricks. Even though my question is not quite fit the scope. However, I really have no other place to find the answer. Hope this will not bother you too much.
    I am using the MSD chemstation as well. It is G1701EA. I am currently running some SCFA samples on GC. And I am wondering if you guys can direct me to find the button to generate a batch report or a sequence summary report. I am able to get the batch do auto integrate and quantitate. However, I could not find a place to generate a single report which have all the compound identified for all 177 samples that I ran.
    Could you please help me with this?
    thank you.

  8. I am not aware of a function in chemstation that is built in to do this. I believe you can build a custom report database, and write a custom report that will generate the data you are looking for. Most commercial laboratories upload the data from their individual samples into a LIMS system, and use this for more complex data analysis.

  9. Margaret says:

    Our Chemstation software is printing reports on only one page no matter how many pages the report should be. I have switched printers and it is still the same, which tells me it is the software. Any advice?

  10. Tom says:

    Is there a way to change the word soil that Chemstation searches for when choosing the surrogate matrix to something else? Is there a macro that I can alter? I have two separate limits for surrogate recovery and do not want the word soil in my raw data because the samples are not soils.

  11. Tom, I’m not aware of a way to make this change in the Enviroquant GUI. The software is highly customizable, but I don’t know which Macro to edit. I used to handle this situation by keeping two slightly different quantitation methods based off the same calibration data. Just change methods when processing data. If you use the “do list” function, you should be able to do this fairly quickly.

  12. Rhi says:

    Hi, is there any way of making Chemstation run on windows 8? I have chemstation version E02.02 which ran fine on my windows 7 computer. Tried installing on windows 8. It is able to install but not fully and does not recognise any of the files.

  13. Jon Walsh says:

    thanks fo the info

  14. Indu says:

    Hi, Can anyone please tell me how to add individual standards in different data files into one database in chem station.

  15. I may be able to help, but need some clarification. Are you talking about a quant database? As in you want to build a calibration using different standards that have different compounds in them?

  16. Indu says:

    Thank you.Yes, I have twenty individual pesticides standards in different data files. I want to add all these calibration curves in to one database. That means I want to quantify all these pesticides all together.

  17. Indu says:

    Hi dear,
    In your chem station view there are many standards in one database. Are there in one mixture or as individual standards? Please reply me soon.I want to add many individual standards which in different data files in to one data base. Please help me to do that. Thank you very much.

  18. Richard C says:

    I have a similar problem with ChemStation E.02.01. But it totally crashes in Windows 7 starter. It says the responsible is ntdll.dll for the data analysis part, and cp.dll for the Instrument control!

    Any idea? I though this version was already compatible with W7!!!

  19. I would call Agilent Technical Support. I think you might need a 64-bit compatible update.

  20. D. Matthew Dukes says:

    @Margaret above, I believe that is a known problem for E.02.02. In our lab, we rolled our E.02.02 back to E.02.01 to fix the heinous pdf problem. When you generate the report, it generates a separate page for each?

  21. Thanks for the info.

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