Automating Batch Integration for specific RTs on Chemstation

[h_sun]

I'm new to using Chemstation. I'm trying to get the peak areas at several specific Retention Times for a large number of samples. I know the RT for all the expected peaks and just want the peak areas for these select RT peaks. What's the best way to do this? Using the auto/integrate function results in a messy data file; the integration picks up too many random peaks from the background and makes data analysis difficult.

I've tried using the 'setup quantitation' but it didn't seem to work. I couldn't even get it to quantitate the internal standard - it was not detected even though there was clearly a nice peak in that retention time range

[lmh]

are you in GC or LC world?
If GC, you need to set up a quantitation method (even if you have no standards and only want peak areas), and then use the "create custom database" bit to analyse all the samples. In LC world you probably want to set up a processing method and use Batch Reprocess.

If you have a clear peak that you can see, but the processing method is failing to recognise it, there are a number of things that might have gone wrong. I'd start by looking at what signal you are quantifying. If it's an extracted ion chromatogram, extract that mass in the file that's not working, and see how big the peak is. Is the integrator integrating it at all, or is it smaller than a cut-off threshold? Is it within the expected retention time window for the named compound? If you're in GC Chemstation, is it expecting qualifier ions at particular ratios, and if so, are they present and correct? In GC world, one of the problems I've come across is that someone sets up the default integrator to see only big peaks using a TIC because they want to use the Autoquant setup, or because they don't want masses of peak annotations written all along the baseline. They then use this in a method that quantifies extracted ion chromatograms, but because EICs look at individual masses, they are all smaller peaks than the peaks in the TIC, so a peak that is seen and integrated clearly in the TIC suddenly vanishes when you try to quantify it. The most obscure version is when the method expects qualifier ions, and one of them, perhaps already small, becomes too small to integrate, and the main peak, which is good and already integrated, is suddenly ignored because a qualifier you'd rarely look at has slipped below the threshold.

What you're trying to do ought to be possible... persevere, it's worth it!

[Peter Apps]

Depending on how many peaks you need areas for, a crude but effective way is to start with integration inhibited, turn integration on just before the first peak starts to rise, turn it off again after the peak is back to baseline, then on again just before the next peak etc etc. Leave a bit of extra time to allow for retention shifts. This is risky with complex chromatograms, but fine of you have baseline resolution for all the peaks of interest.

Peter

[h_sun]

Thanks for the replies! I'm doing GC.

@lmh - I didn't setup my quantitation database until after I ran my samples. Do I need to reprocess the samples with the new methods file with the updated quantitation database?

[Yama001]

Yes, you will need to reprocess (Calculate and Generate Report) the previously acquired data files.

[lmh]

If you're new to Chemstation and using the GC version, there's just one thing I'd warn you. Chemstation has a habit of remembering a peak area once it's integrated it. If you go back later and try to change a method so that it will integrate a peak differently, you may find that when you create a custom database, it doesn't take the new integration into consideration, and just produces the same peak area as it did before (certainly for all the files that you haven't looked at directly, and have merely reprocessed in creating a database). I think this is because Chemstation dates back to an era when computers were slow, and integration was hard work, so it made sense to remember rather than reintegrate.

If this happens, you can save your method with a new name. At some point Chemstation will produce an innocent-looking pop-up window asking you what version of the results you'd like to use in your new method. Absolutely, definitely, cancel this window by clicking on it's close X. You may even get a couple of such windows. If you've done everything properly, you should find that all calibrated levels have vanished, and create a database is now greyed out. You will have to "update one level" at least to make it possible again. This creation of a new method forces Chemstation to use the new method's parameters to reintegrate everything from scratch.

If anyone knows a more elegant way to do this, I'd be very, very grateful.