Obtaining mass spectra of rider peaks

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

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When trying to obtain the mass spectrum from a smaller peak on the slope of the matrix peak what is the best approach? How much does subtracting the matrix peak from the rider peak impact the accuracy of the mass spectrum of the rider peak? I attached an example TIC from my current analysis. My thought is that some mass fragment ions may be inaccurately represented in the rider peak due to the matrix peak. Is it better to subtract from baseline outside of the matrix peak? Thanks in advance.

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This seemingly innocent question is actually a very nasty one!

That is because it is easy to do it wrong, and difficult to do it right.

I would approach it this way.

First, be aware that to get the best signal-to-noise (S/N ratio) it has been shown that only those scans with intensity above 38% of the peak height should be summed [Anal. Chem. Z. Zhang and J.S. McElvain, 1999, 71, 39-45].
Baseline of peak of interest (PoI) is at about 400,000 counts
Maximum of PoI is at about 2,000,000 counts
So, peak height is about 2,000,000 - 400,000 = 1,600,000 counts
38% of 1,600,000 = 608,000 counts.
So, only sum those scans that have an intensity of 608,000 + 400,000
= 1,008,000 counts or greater.
This gives you the crude mass spectrum at RT 10.62 min.
Try to identify important ions, such as [M+H]+, [M+H - H2O]+, [M+H - ROH], [M+H - RCOOH]+ etc.
Plot each of these to see if they occur only in the PoI, or are also present in the matrix.
Check also their possible occurrence at RT 10.89, 10.50 and 10.82 min. (possible isomers or structurally similar compounds).

Use this info to locate two clean regions of the background, one at either side of PoI, that can be safely subtracted from the crude spectrum of PoI.

Regards,
JMB
You are welcome!
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