Hello!
I'm having difficulties comprehending how MS and MS/MS spectra are obtained in regard to eachother.
In easy words:
A package of ions ("package 1") is eluted from the LC and MS spectra are obtained from these ions. From these spectra, the most abundant ions are chosen for further dissociation for MS/MS spectra. My question is: the ions used for dissocation is coming from a different package ("package 2") of ions eluting from the LC, since the "package 1" has already been used for MS. How do we know whether the ions chosen for dissocation, based on the MS results of "package 1" can also be found in "package 2"?
The ion packages are made in much shorter time-scales than the elution time of the LC peak. So you can have many packages from same substance/peak.
First off the ions are the same, just changed - it's not like the mass spec has to 1st "see" the ions then decides on dissociation. It's all done on the same ions. Lets take caffeine as an example, the positively charged ion has a m/z of 195 and the most abundant fragment is m/z 138. The 1st quad is tuned to 195 - the caffeine ion travels through the 1st quad, then passes through collision cell, it is fragmented resulting in the 138 ion - which passes through the 2nd quad and subsequently detected. The parent is caffeine and the daughter is the fragment 138. They name it like this because the fragment (138) actually comes from the parent (195).
Your "package" in terms of mass spec is actually called a scan. Mass specs have a very fast scan rate (how fast a package goes through the mass spec)- this relates to how fast a mass spectrometer "sees" the ions (packages) passing through the quadrupoles. If you took your peak and sliced it up into 20 pieces one of those pieces would constitute one scan. Most MS/MS systems are able to scan at a rate of 10-20 scans per second depending on the m/z range of your acquisition parameters. If you think about this in relation to the time it takes a peak to elute from your column (peak width), you will realize that there is abundant time for the mass spec to easily accomplish the task, and can do it on multiple target compounds eluting at the same time. To verify this zoom in on one of your peaks and using the software determine how many scans the peak is made up of. A good chromatographic peak requires a minimum of 10 scans across the chromatographic peak. Pull up the performance specifications of the mass spec you are using, and look at the MRM acquisition rate - it's likely to be in the range of 250 MRM data points per second.
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