MSD Chemstation trying to "Quant" a non-existant substance.

[lgc_andy]

Hi,

I'm a LIMS developer trying to diagnose an issue with MSD Chemstation. I'm not totally up to speed with the science & terminology behind GC-MS and the lab technicians aren't experts in MSD Chemstation - they just know the bits they need to do the job. Normally between us we can work through issues, but this time we're asking for help!

We’re using MSD Chemstation on Windows XP and Windows 7. The versions in use vary by instrument (we have 7 GC-MS instruments): The lab technicians tell me the following versions are in use:
D.0200.275
D.01.02.16
E.02.01.1177
E.02.02.1431

The instruments are integrated with a LIMS system (Labware LIMS v6) – this has been done by editing the “deuser.mac” file of each method to call a separate macro to copy the result files to network folders.

We are experiencing an issue with our “Drugs Search” method. This is a qualitative method to determine if any controlled substances are in the sample. Sometimes the “deuser.mac” doesn’t seem to execute and therefore the results don’t get into the LIMS system. We have narrowed this down to the following situations:
• When a BLANK sample is run (and no drugs are found in it)
• When a normal, analytical SAMPLE is run (and no drugs are found).

In both cases, an error is displayed in the status bar:
“An error occurred in quantitation reporting : Compound not found in quantitation database”

Now, obviously if no compounds are found then there is nothing to search for, quant wise. But the main question is: Why is it attempting this at all? The method is not supposed to be doing any form of quant (we have other methods for that). On samples (or blanks) when drugs are detected, this error doesn't occur. But no "quant.txt" file is created either - which correct for this method, but doesn't quite fit with the error message!

How can we stop MSD Chemstation from trying to quant a compound when none have been found?

Andy

[chemstation]

Hello Andy,

I am going to make an educated guess that they are using EasyID or QEdit to find the compounds, and these use the Quant database, hence why you would get messages related to Quant.

Now, obviously if no compounds are found then there is nothing to search for

this is the wrong way around. Chemstation has done then search, and found no compounds.

hence when you instruct the macro to produce the Quant report, it reports back there are no compounds to find. So of course it doesn't produce a report.

whilst there are several methods to work around this issue, I am surprised of the way that they appear to be running the samples.

The issue is, Where is their internal standard? They must be running one.

Thus when they include their internal standard in the QEdit, Chemstation will always be able to search and find at least one compound.

IMHO I would ask the lab staff to include the internal standard in the Quant report, thus any future failures must relate to a failed extraction, or failed instrumentation eg bent needle, blown filament etc...

kinds regards
Alex

[ryan.edwardson]

Hello Andy,

I am going to make an educated guess that they are using EasyID or QEdit to find the compounds, and these use the Quant database, hence why you would get messages related to Quant.

Now, obviously if no compounds are found then there is nothing to search for

this is the wrong way around. Chemstation has done then search, and found no compounds.

hence when you instruct the macro to produce the Quant report, it reports back there are no compounds to find. So of course it doesn't produce a report.

whilst there are several methods to work around this issue, I am surprised of the way that they appear to be running the samples.

The issue is, Where is their internal standard? They must be running one.

Thus when they include their internal standard in the QEdit, Chemstation will always be able to search and find at least one compound.

IMHO I would ask the lab staff to include the internal standard in the Quant report, thus any future failures must relate to a failed extraction, or failed instrumentation eg bent needle, blown filament etc...

kinds regards
Alex

Hi Alex

I'm one of the analysts from this lab. Thanks for replying to this comment.

When a datafile is being run as a 'sample' we are getting the error of 'an error occurred during quantitation: No entries found in the quantitation database'. This is confusing as, to our knowledge, we aren't asking for any quantitation to be done!!

This is mostly occurring when there are peaks present in the chromatogram - we have started using internal standard over the past few months and it hasn't made a difference.

Is there something obvious/simple that we have missed during method set-up that is ticked when it shouldn't be?

It doesn't occur when we run our samples as 'blanks' - I assume because the quantitation step wouldn't be set up to occur for a blank because it wouldn't matter what was in there?

Any help at all would be welcome

ryan

[chemstation]

Hello Ryan,

You haven't mentioned if it finding the internal standard in EasyID/QEdit.
eg do to integration parameters, area reject, RT shift, etc...

If you inject a blank solvent with the internal standard as the only peak
, classify it as a sample, does it produce the same error.

I noticed in your other post, that you are running a custom macro, and I suspect in the Deuser.mac, that it is differentiating between sample and blank as to which sub-routines to execute.

Kind regards

[ryan.edwardson]

Hmmmm I hadn't thought of trying it that way around. I will give that a go and see what happens

As I said I wasn't around when things were set up and our instrument specialist is unfamiliar with the precise inner-workings of Chemstation (having used other instrumentation/software previously) so I'm not totally familiar with QEdit etc. We run our samples and our method then manually checks each peak which is integrated against a number of our own libraries.

Currently if I inject anything as a 'blank' it integrates all of the peaks and creates a report using our macros perfectly fine, which is what makes me think it might not be a macro issue. It follows everything through when the type is selected as blank, but when we inject it as a sample the macros don't seem to work. However I have to go and select the datafile from data analysis and manually run the custom analysis from there, which then runs our macros and creates the report.

From this way of looking at it, it appears to me as though the initial run is being terminated by chemstation before getting to our macros. If I select run method it comes up with an error (different on each machine). Or it could be that when originally run it differentiates between blank and sample, but when 'manually analysed' from data analysis it doesn't make this differentiation and allows it to work.

I think we might be at the point where we have to just re-write the methods new and build from scratch!

[James_Ball]

In the Data Analysis window are you using the Quantitate menu or the Method menu?

It sounds like you are using the Method menu and Run Method, which I have never actually used for processing data. If you use the Quantitate menu, you can setup integration parameters and then enter the ions of interest for your Internal Standard, then follow that with your analytes of interest using retention time, ions for quantitation and qualification and calibration information. This will allow you to process against a calibration curve and quantitate results for your analytes. When it returns the error “An error occurred in quantitation reporting : Compound not found in quantitation database” it is refering to this database that you create for known targets of interest. If you don't create the list of compounds with their information then it tries to quant against an empty database.

If you run through "Edit Entire Method" in the instrument control window and find the box checked for generating a report, then each time a sample is run it is trying to automatically generate a report against the quant database created in Data Analysis. What I normally do is setup an instrument method to gather the data but turn off all of the data analysis options, so that the instrument sequence simply acquires the raw data. I then make another method in Data Analysis that is for quantitation only, that way if I need to change an instrument parameter I don't worry that I will mess up my quantitation method and vice versa. It also makes it easier if I run several different sample types using the same instrument method, but each sample type contains a totally different list of analytes. That way I only need on set of instrument parameters, but I can have many methods with quantitation lists and settings.

[ryan.edwardson]

Thanks James

This, I think that this along with the other topic you're replied to me on, has got me understanding just what that I going on with that select reports menu.

We're a volume identification lab, we use other techniques for quantification, so all we need is a list of peaks with the RTs and the designation that the MS gives them against our libraries (which I think comes from our own macros, rather than the software itself).

Time to investigate!

[chemstation]

1) Are you using QEdit ?

2) If you are integrating and only doing library searches, Doesn't MA & MDMA co-elute.

3) Are you using Chemstation in Enhanced Data Analysis or Enviro/EPA mode.

[ryan.edwardson]

Hello

I think I've figured it out.

All the 'analysis' part is done by our macros, not using data analysis (except for the quants which we do use the quant report for). Basically our methods had the 'custom report' and 'update custom database' boxes ticked when we don't have these reports or a database. This was preventing the process from getting through to our macros (which run after these events) and stopping our analysis from happening.

I've now gone into all our machines and all our methods (except quant) and unticked everything. This has (I think - fingers crossed) solved all of the issues.

Many thanks for your advice and assistance in understanding how chemstation works - we'd been looking around the right area for a while but a basic misunderstanding around the 'custom report' meant that we just couldn't solve it.

Also - our methods have been tweaked for that MA and MDMA don't co-elute but we also use a derivitising agent on another run to separate them further