Area of INDIVIDUAL ions in peak?

Discussions about GC-MS, LC-MS, LC-FTIR, and other "coupled" analytical techniques.

7 posts Page 1 of 1
Hi Chromatography Forum.

For my bachelor's thesis, I ran competition experiments between two substrates. One has a deuterium instead of a proton (mass = 1 higher). As you can imagine, the peaks of the two substrates are basically on top of each other, so area integration gives no useful information.

I've read up on TIC and as far as I can understand, TIC sums up the intensities of each ion. So I want to know if it is possible to get the area of just a single ion fragment (i.e. m/z = 187) out of the full peak which contains ~20-30 fragments?
And if so, do you know how to do it in Postrun Analysis? I've spent hours in the software and the manual, but I cannot find it...

Thank you so much in advance!
Can you tell us which kind of instrument this is?

In the software I work with, it's called "extract mass" or "show mass X".
Thanks for your response. The instrument is a Shimadzu GC-MS, I'm not exactly sure of the model and column type etc., I can check when I'm in the lab later today.

What software are you using? If it's easier in that program I may try it out. Postrun analysis seems not super user-friendly! I attached a screenshot of the user interface below (click to enlarge). The black area curve is the standard GC-MS peak of all the ions. I've been able to find the pink, blue, brown and green TIC peaks of the individual ions that I'm interested in (186, 187, 188, 189), and it really does look like they have an integrated area, so it seems like it should be possible to find their areas. I just haven't been able to find the function.


I use Shimadzu's software only in an LC environment, so I might be wrong about this in GC. It looks to me as though you're using an older version of Shimadzu's software, in which case try right-clicking on the chromatogram to get the drop-down menu, and look for "Fragment table". If you have it, click on it, and it will bring up a dialogue where you can choose which TIC's to display (or tick "none") and underneath that, a table in which you can enter signals you'd like to see as chromatograms. They can be TIC, BPC (for base peak) or a mass entered as a number, in which case you'll get the extracted ion chromatogram. You can also scale them so you can compare peaks of very different intensities.
Shimadzu's software is quite powerful, but not intuitive - it's a really good idea to get hold of the manual and have a good browse. I keep finding things I didn't know existed.
edit: I should add that of course you can enter individual masses in the compound table, so that the software will integrate the area of extracted ion chromatograms and quantify a single mass. You will then see the extracted chromatogram with any smoothing and processing at the bottom left, underneath the spectrum, in the bit that you've got shrunk quite small in your screenshot. That is another feature of Shimadzu's software: there is a lot going on on the screen, and a large screen with good resolution will pay dividends.
If you look at the picture you posted, you already have the ion traces of 186, 187, 188, and 189 there. What you need to do ist to set up a quantitative method.
If you close your little "Qualitative Table" window, you will get to the compound list. Click "Edit" and fill in the names of your compounds, the ions, the retention times and the concentrations of your standards.

Actually LabSolutions is not bad - you have to get used to it. The F1-key is often quite useful...

P.S.: you data rate is too low. You need at least 10 points across the peak for reliable quantitation. You have like 5...
Thank you so much for your detailed responses guys! After some fiddling around with the compound table I finally managed to do it! It is a bit difficult to navigate the program when you don't have a lot of GC-MS knowledge in general, indeed.

Yeah H. Thomas I see your point and I agree - there are only 4-5 "scans" for the entire peak, so splitting it up leaves only 2-3 scans for each compound I want to isolate, it does not seem like the optimal way to get results :) But either way, we are just working on our bachelor's thesis, so we are not even allowed to change the settings on the instrument or anything like that, and it still seems like we can get decent data this way.
We ran a competition experiment between a deuterated and non-deuterated substrate, so we have about 13 spectra in which to analyze the ratios between the two compounds (which are both in the same peak).

Anyways, you helped me to locate exactly what I was looking for and quickly - niche forums are great!

Thank you again and have a good day :)
Balinbalin wrote:
Yeah H. Thomas I see your point and I agree - there are only 4-5 "scans" for the entire peak, so splitting it up leaves only 2-3 scans for each compound I want to isolate, it does not seem like the optimal way to get results :)

If your peaks are co-eluting with 5 data points in TIC (full scan), you will still have 5 data points for any mass you "extract" from it. You can see it nicely in your picture: the data points of the different masses fall on the same vertical line. The way it works is that the instrument is set to collect all masses from a certain range (specified in the method) for x milliseconds (specified in the method), and then repeat. Each cycle gives 1 data point. If your peak is for example 5 seconds wide, and it collects data for 1 second before repeating, you will have 5 data points.

Another thing I'd like to note in your experiment. A difference of 1 in mass (1 deuterium) is in my opinion tricky for an internal standard in low-resolution MS. I'd advice to run a sample with only the internal standard on one hand, and a sample with only the target component on the other hand. See what signals you get for the other component in those samples.
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