Chromatography Forum

Let me start by apologizing for asking such a fundamental question. In Enhanced Data Analysis I see 2 windows.
There is a (2) TIC: samplenamehere.D\data.ms
Below that is (3) TIC: samesamplename.D\datasim.ms
It appeared that the information was representing the same sample only in a different scale/amplitude... BUT when I view the ions of a clean sharp peak in the top (2) TIC window - they differ significantly from the ions of the same sharp peak found in the bottom (3) TIC window!? What am I looking at? I gather that the bottom is SIM mode... but I don't understand why these plots of the same compound show such different ions.

Any help appreciated.

Let me start by apologizing for asking such a fundamental question. In Enhanced Data Analysis I see 2 windows.
There is a (2) TIC: samplenamehere.D\data.ms
Below that is (3) TIC: samesamplename.D\datasim.ms
It appeared that the information was representing the same sample only in a different scale/amplitude... BUT when I view the ions of a clean sharp peak in the top (2) TIC window - they differ significantly from the ions of the same sharp peak found in the bottom (3) TIC window!? What am I looking at? I gather that the bottom is SIM mode... but I don't understand why these plots of the same compound show such different ions.

Any help appreciated.

I assume you've run a mixed SIM/Scan acquisition method... the top window (data.ms) is the plot from the Scan mode, which will include every ion that shows up in your selected scan range in the TIC, which is why you'll see extra ions there.

The bottom window (datasim.ms) is the plot from SIM mode, which will only show ions from your SIM selection.

The bottom being the SIM selection - I understand you to say that ONLY the ions which are in my calibration table, the target max abundance ion, and the other 3 qualifiers will display when I double click on the peak showing in datasim.d window. *What does not make sense with this is when I change the target ion of my peak in the calibration table with the max abundance ion in scan mode, and save the method, then recalculate - I don't get that new target ion when I double click on the datasim.d window and my peak!? I still get the same ions revealed.
Now I did not re-aquire data after making this change. I just thought OK, change the ions in the calibration table to the scan mode ions, and those new ions should be shown in my datasim.d peak. Something is still very much lacking in my attempt to understand this analytical technique.

Please be patient.

The information in the datasim window will come from what is programmed into the SIM portion of the acquisition method. Any changes in the data analysis portion will not change what is displayed in the datasim window.

SIM doesn't filter Scan after acquisition, it filters during the acquisition of the data, so to change what is in the window you have to re-acquire the data. When you edit the Mass Spec section of the acquisition method you will have a drop down menu near the center of the screen to choose Scan parameters or SIM parameters, choose SIM and look at the masses listed for acquisition, they can be all the same across the run or can be in timed segments if there are too many to acquire at once. That will be what you see in the datasim window in data analysis.

From the information you have so graciously volunteered, I started looking through the method that the previous chemist left before leaving the company, and I find 2 SIM Groups a couple of minutes apart. Each SIM group has a couple of peaks (active ingredients) in our standard solution. The ions look like this is the reason so many of each of the different peaks have the same ions. The solution is to do a scan mode to pick out the most abundant ions, then make groups for each peak having their unique ions. Then reaquire data with a new run. Am I understanding correctly?

Thank you so much for your time! We do not have any source for questions since our chemist left the company.

That is exactly how you develop and SIM method.

Using SIM does two things for the final analysis, it improves sensitivity since you are focusing on just the masses you need to quantify and qualify the target, and it eliminates the noise from background contamination or any other interfering compounds that may be present.

It works great for analyzing samples where you know what should be present. It does not work for analyzing samples where the targets are unknown, that is best done by full Scan mode.

There is also the option on some instruments to do SIM and Scan simultaneously, so you get the best of both worlds, with a small trade off of lower sensitivity. This only works on instruments that are 5973(with fast scan electronics, so later models) and up in the Agilent line. Not sure about other brands of GCMS.