Chromatography Forum

I have probably a silly question here:

How can I extract an ion from a SIM trace in Chemstation which contains more than one ion (i.e. group)?

The only thing I can see it's the summed intensities of the different ions. I basically want to see them separately.

I manage to integrate a specific ion at a set retention time, but it's not what I want.

How can it be so hard?


Thanks

-T.

If it is the GCMS Chemstation

Third menu across is Integrate

Third item down is Ion Chromatograms

Open that and enter the ion or ions you wish to display and hit Ok and it will display each ion trace in a separate window.

It does seem odd to put a chromatogram display window in the Integrate menu, but that is where it is.

thanks for your quick answer.

I have tried this before but what it displays is just the ion from the TIC not from the SIM!! (I am acquiring in both scan and SIM mode). I dunno how to tell the software to extract from datasim.ms rather than from data.ms

t.

From the help search on Chemstation

Extracted Ion Chromatogram
An extracted ion chromatogram (EIC) is a trace of a particular mass or mass range from data acquired in either Scan or SIM mode.

I think it will display from the SIM data set if you do a SIM only run, but I am not sure how to get the second signal to extract if you are running simultaneous SIM/Scan. I don't have any combined data handy to test, but I can possibly look up some old runs and see what I can figure out.

In older versions of Chemstation you could manipulate the data stack to put different sets of data at the top of the list, but not sure if you can still do that. If so you could move the SIM data ahead of the Scan data and possibly make it work. If I had the time I would search through the macros that drive data analysis and see if I could find how that is coded since each of the menu items is pretty much a macro that is in the macro directory.

Isn't the EIC of a particular ion the same whether it is extracted from the SIM or scan TIC? (Sorry if that is a silly question - I don't have much experience with SIM/scan)

Hello

Isn't the EIC of a particular ion the same whether it is extracted from the SIM or scan TIC? (Sorry if that is a silly question - I don't have much experience with SIM/scan)

The sensitivity is different for SIM and Scan so ions response in SIM is totally different than from Scan.

Regards

Tomasz Kubowicz

@James_Ball

so I gave up on Chemstation and moved to Masshunter. Masshunter does exactly what I was looking for. There must be a bug or something in Chemstation. But if you figure it out please let me know


T.

I think there is a menu option that will allow you to choose which set of data to use (there are actually two data files in the folder - data.ms and datasim.ms). I have not used the combined sim/scan in a while so I do not recall exactly where this is - it may be an icon rather than a menu item. I think the data analysis must be configured in "enhanced" mode for this to be available.

I think there is a menu option that will allow you to choose which set of data to use (there are actually two data files in the folder - data.ms and datasim.ms). I have not used the combined sim/scan in a while so I do not recall exactly where this is - it may be an icon rather than a menu item. I think the data analysis must be configured in "enhanced" mode for this to be available.

That may be where I am missing it since we run in Enviroquant mode instead of Enhanced mode.

I think there is a menu option that will allow you to choose which set of data to use (there are actually two data files in the folder - data.ms and datasim.ms). I have not used the combined sim/scan in a while so I do not recall exactly where this is - it may be an icon rather than a menu item. I think the data analysis must be configured in "enhanced" mode for this to be available.

That's the right answear.
From the menu: File > Select signals > ... and checkmark signal(s) you want