Chromatograms subtraction with ChemStation

[NINA Cla]

Hi,
I work with a GC 7890A - 5675C MS detector (G1701EA ChemStation).

Premise that it is a strange request, i need to use the MSD "as it was a FID".
I'll explain: we analyze volatile aliphatic hydrocarbons in soil samples and we express the result as the concentration corresponding to the sum of all the chromatographic peaks between n-pentane and n-dodecane (we use Area Sum integration event). We consider only the TIC window and we need to be able to subract a blank chromatogram from a sample chromatogram. We also need to be able to integrate the resulting chromatogram and to generate a report from it.

Thanks in advance

Nina

[chemstation]

Hello Nina,

for the following to work, the RT of the peaks need to match exactly!

Load the background data file.
under Options, Show Command Line

type in the command line stack

type in r9=r0*-1

load the data file of interest

type in r8 = r9+r0

type in r0 = r8

type in draw 2,r0

then integrate

you can automate the above macro commands
under Options, Custom tools
by clicking on the "Hammer Icons", you can assign one icon to inverse the TIC of
the background data file, and another icon to add them together and display the
results, plus heaps more options,
Get your supervisor to support this, as the RT matching is going to be your biggest
issue.

Alex

[kubowicz.tomasz]

Hello

You can also subtract "background" file from each run (it is good and quick method when you don't have long sequences). You can create your own custom report and optimize all things you need for report (tables, sum area report etc).

Regards

Tomasz Kubowicz

[NINA Cla]

Thank you Alex,
I'll try your method.
I tought about the RTs but, probably, running a blank immediately before the sample there will be no big problems. We usually perform short sequences.

Could you suggest me a guide where can I find a list of the possible commands by typing in the command line?

Thank you again
Nina

[NINA Cla]

Hi again,
I've tried the use of the command line in order to subtract the blank chromatogram from a sample chromatogram.
I obtained the desired resulting chromatogram and I'm able to integrate it manually but when I ask the chemstation to quantitate the file automatically the generated report is reported to the original chromatogram and not to the subtracted one. Is there a way to avoid this problem?

Thanks
Nina

[chemstation]

Hello Nina,
It will not work for Quantitate->Calculate.

1) you can copy the Integration results to the clipboard, and paste into excel.

or

2) Use the inbuilt Database in Chemstation,
that produces a file that can be opened in excel where one
line is for the background, and the next line from the sample.

I did write a programme that would subtract one file from another, but the
slight change in RT always gave false "Isotope Peaks".


Kind regards
Alex

[lmh]

chemstation is right, subtracting one run from another is almost always disastrous because even the tiniest variation in retention time can create false peaklets at the edges of peaks. Little distortions can disturb the integrator's efforts in finding the base-line, and the areas of the peaks become rubbish.

If you're worried about your peaks in samples being contaminated by something that wasn't in the injection, and that's why you're subtracting a blank, why not just integrate the blank run, and subtract its peak areas from the relevant peaks in the integrated sample runs (i.e. do all the subtraction at the level of integrated compound lists, in Excel, rather than at the level of raw data in chemstation)?

I know you know this, but a TIC from an MSD isn't an FID trace and never will be...