Building a Calibration Table in Ancient MSD Chemstation – Part 1

g1701aa.03 enviroquant about

Some of the feedback I received after my last post was that most of the small environmental labs out there are still running 5971 and 5972 MSDs off the old G1701AA.03 software, and that demonstrating data processing techniques in G1701EA.02 may not be relevant.  Fortunately, we still have a 5890/5971 in the lab.

most sensitive mass spectrometer

Unfortunately, we are controlling this instrument from an old computer running Windows NT 4.0 and MSD ChemStation G1701BA.00. In order to demonstrate A.03 functionality, I had to run down a working copy of Windows 98 and install it in a virtual computer in Windows 7 because G1701AA.03 requires a 16 bit version of Windows. Officially, HP only supported Windows 95, but Windows 98 Second Edition was an extremely stable OS, and my old lab had good luck running the software on this platform.

Today’s tutorial will focus exclusively on the EnviroQuant version of A.03, and will cover populating the calibration table with compounds using a few compounds from the first internal standard group of EPA Method 524.3. We will deal exclusively with the initial calibration menu (InitCal) which is shown below, though “save method” is found under the File menu.

enviroquant menu initcal a.03

First, you will want to set your calibration’s global parameters, and this is done under the “Set Up Quantitation” menu option. There are a few things worth mentioning here. The default integration parameter file is events.e; you can create specific integration parameters for specific compounds, but you’ll want to enter your default integration file here so you don’t need to type it in for every compound later. The same goes for the rest of information in the New Compound Info box below.

Quant Database Globals

Once you are satisfied with your selections for the Quant Database Globals, click enter, and the Edit Compounds dialog box should appear.

a.03 edit compounds

Click “Insert Above” and this brings up the “Quant Setup” interface (shown below), where you can select peaks by double right clicking them, name them, and select quant and qualifier ions. Personally, I don’t like this interface, and prefer manually entering the compound info. Generally, I deal with large compounds lists (like 8260 or 8270) and find the peak selection process tedious.

quant setup a.03

If you go back to InitCal menu, and select “Edit Compounds,” the same Edit Compounds dialog box from before appears, but this time, when you click “Insert Above,” you should see the first page of the compound info screen. If you already know the elution order of your compounds, you can enter them one at a time.

EPA Method 524.3 – Table 4 lists the recommended quantitation ion and associated internal standard (IS) for each of the target analytes. Make sure you change the Quant signal to “Target Ion.” If you don’t know what qualifiers to use, you can look up the EI mass spectra at the NIST website.

compound info page 1

Generally, when choosing quantitation and qualification ions, you will want to use the M+ molecular ion, the C13 isotope (M+1)+ or halogen isotope (M+2)+, as well as an ion that can be explained by a common mechanism, such as the loss of a ring, halogen, or hydrogen. The mass fragment with the highest response does not always make the best quantitation ion, especially if it has a relatively low m/z (less than 50) because there is commonly high background responses for these ions.

This is a good stopping point. Next time, we’ll configure internal standards, matrix spike compounds, and surrogates for automated data processing by the quant macro.

One Response to “Building a Calibration Table in Ancient MSD Chemstation – Part 1”

  1. Jonathan Price says:

    Have you finished part 2 of the setting up quant table in old enviroquant? If so, where can I find it? This is very helpful article.

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