Hi James,
Generally, I agree with your conclusions.
1. Yes, Ar dimer is something inherent to the instrument. There are 1-2 settings that your Fluidigm engineer can adjust to (slightly) alter your Ar dimer signal, but you cannot get rid of it. Frankly, I find it useful to have as positive signal: if Ar dimer goes away, there are significant issues with the instrument's overall signal/sensitivity.
2. Iodine, Barium, and Lead are probably the 3 most common contaminants, in my experience. They often come from buffers used in staining or cell isolation, or from the water used. 3% nitric acid (or Tuning Solution, which contains 2% nitric acid) does the best job of stripping them out of the system.
3. Yes, Xe is always present in Ar: they're both noble gases present in air. Argon boils at 87K, while Xe boils at at 165K. Xe is present at a much lower concentration in air than Ar (
http://scifun.chem.wisc.edu/chemweek/GasesofAir2017.pdf), so it's probably not economical to separate it out unless there's a *specific* reason to. Liquid Xe is also more dense than liquid Ar, so it settles in the liquid dewar and does generally increase toward the end ("heel") of the liquid tank. I haven't seen much, if any, variation in Xe signal over the course of a compressed gas cylinder.
Again, I like seeing the Xe: i the Xe goes away, that usually means that there's a problem with the instrument (usually liquid sample flow problem; for some reason, the Xe signal in wet plasma is higher than the Xe signal in dry plasma).
The main issue with Xe is when you get a "bad" tank where the Xe levels are too high. The machine uses Cs133 in the Tuning solution in the Mass Calibration process: it has a small TOF "search window" around the expected Cs133 arrival time, and mainly locks onto the brightest signal in that window. If the Xe132 or Xe134 signals are too high, it has trouble, and ideally refuses to calibrate (so Tuning would fail at the Mass Calibration step). The software has a default max Xe signal for this reason.
4. Correct, the machine doesn't know what an element is....it only knows that ions are arriving in a time window that you have calibrated to mean a certain mass signal. So, it can't tell the difference between Cd110 from a Qdot and Pd110 from a BC agent, or from Gd155 vs La-oxide.
5. Generally yes: however, don't forget oxide spillovers.
Detector aging does happen. This is one reason why you don't want to run really streaky samples, as the streak ions are still hitting the detector without you getting "useful" data. Also, the more channels you use and the more metal signal in each channel, the more ions hitting the detector and the faster it ages. This is definitely one reason why you want to titer all your reagents (including BC agents, Live-dead, and Ir intercalator).
Yes, even if you're not measuring all possible channels, all ions present in the sample in the measurable mass range hit the detector, and therefore contribute to detector aging. This is the difference between watching your sample in Masses view vs TOF view. This is also why I generally watch my samples in TOF view, to be able to detect background signals in other channels *not* being collected. First, because I just want to know if there are other contaminants. Second, occasionally those "absent" channels contribute to signal in "measured" channels.
For example, I don't normally have a probe on La139, so I don't normally collect that channel. However, a couple years ago, I had a sample that was (unknown to me or my customer) hideously contaminated with La139. The La139 signal was so bad that it looked like a solid black Sharpie line in TOF view. The La138 signal was also almost a complete line, and even though there's no La140 isotope, the right-leg spillover from the massive La139 peak was noticeable in the "Ce140" bead channel. Additionally, the Gd155 channel was super-streaky as well, due to the massive La-oxide spillover.
Since I had a weak marker like CCR6 in that channel, I basically couldn't interpret that channel in that sample.
Mike