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GC/MS in SIM mode: the baseline is just like steps
Posted: Thu Sep 08, 2016 4:04 am
by thohry
We are using Agilent 5977 with MassHunter.
When ever we run SIM mode (at low concentration), the baseline is not smooth, but up and down.
Any one know how to settle this or we have to accept it as master of course .
Thanks for any input.
Here is an example:
Re: GC/MS in SIM mode: the baseline is just like steps
Posted: Thu Sep 08, 2016 6:07 am
by dblux_
Don't change SIM ions during runs and you won't get steps
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(Probably you will have to accept these "steps" as changing SIM ions during runs is a result of your method optimization.)
Re: GC/MS in SIM mode: the baseline is just like steps
Posted: Thu Sep 08, 2016 6:50 am
by Hornet
In SIM mode you have different windows where you monitor one or more ions.
In every window you have different ions to monitor and you see the step up or downs because you start from a window monitoring for example m/z xxx that has his noise, then you start another window with m/z yyy which has a different noise which can be higher or lower. For example you are monitoring a ion with m/z close to column bleeding m/z and of course you'll get higher baseline compared to other windows.
Davide
Re: GC/MS in SIM mode: the baseline is just like steps
Posted: Fri Sep 09, 2016 8:25 am
by thohry
Thanks
It seems there's no way to do anything about that and we have to accept the 'steps' as a matter of course ?
Re: GC/MS in SIM mode: the baseline is just like steps
Posted: Fri Sep 09, 2016 8:42 am
by Hornet
Thanks
It seems there's no way to do anything about that and we have to accept the 'steps' as a matter of course ?
I don't see any problem in that, unless you are doing mixtures quantification and in that case you need a stable baseline for integration but that's not what you do in SIM, or you could do it in SIM by monitoring all the m/z of interest in the same section, but you are losing signal or peak quality.
There could be an alghoritm that smooths the baseline and takes all the step to the same level, but i never used it if it ever exists and it would be just a mathematical operation.
Re: GC/MS in SIM mode: the baseline is just like steps
Posted: Wed Sep 14, 2016 9:17 pm
by James_Ball
Pretty much you have to accept that SIM has steps in the baseline. Since most quantification takes place in a small time window and displays only the ions of interest you normally will not see it when evaluating data. If you are trying to make a chromatogram with a baseline that most other people are used to seeing, well it is time to educate them to what is "normal" when looking at SIM data unfortunately.