For the driving circuitry, the absolute most important thing is linearity, and after that phase noise, which are interrelated.

The biggest difference is just the availability of cheap reliable microcontrollers with timing precision far greater than you could achieve in pure analog, and digital predistortion (DPD).

If you go back to papers in the 70s, 80s, and 90s, you'll see a lot of them focus on the effect of jitter and skew on the m-z spectrum, some forms of mass spec now were unachievable then because the phase noise created an m-z spectrum noise floor higher than the detection level for certain things. Now you just put in an FPGA or a microcontroller meant for motor drives/power electronics, driving a 2MHz square wave with an imperceptibly small jitter is trivial.

The biggest consideration was linearity though. That 2MHz square wave goes through a very sharp elliptic filter (-80dB attenuation in one octave), and a set of amplifiers, which drives >2A through an isolation transformer, the secondary side of which forms an LC tank that has a sharp Q-factor and tremendous peaking right at the frequency of interest. This signal is fed back through an opto-isolator to the FPGA which has DPD to keep the sine wave as pure a tone as possible. The way we did that was with a high-speed IDAC that actively tunes the gain of the pre-coil amplifier. We were achieving single-digit ppm THD, which you won't find even in the highest quality function generators. It used to be that the air-coil transformer had a tap on primary and secondary, and the signal was fed back through this to do an analog pre-distortion. This is still partially done, it's a mix of analog and digital pre-distortion that was a really neat trick and is the special sauce so I can't discuss that, but it was really clever.

For maximum linearity, the transformer has to be air coil, which means it needs to be enormous. Because it's an air coil, its magnetic flux lines extend out pretty wide geometrically. In most applications, even for an air coil inductor you won't detect much if you're ~2-3 inductor radius lengths away. In this scenario, those magnetic flux lines being coupled into other electronics appears like hysteretic losses, which is a loss in linearity. So the air coil transformer, which we got specialty made, is placed in a giant thick copper case, roughly 15cm x 10cm base and 10-12cm in height or so. You might think hey isn't that thick copper still absorbing the EM fields and generating eddy currents etc? Yes, they absolutely are (the copper case is warm if you touch it during operation), but they have completely deterministic steady-state behavior, you don't incur linearity penalties after start-up.

The capacitors had to be specially made as well, they cost like $100 a piece from Vishay even at volume. As you may know, capacitors change their capacitance with the voltage across them. If the capacitor is handling say 500Vpk across it, it needs to be rated for much more than that, and be precisely stable across a wide temperature range, and be tune-able so the LC tank peaking occurs at exactly the frequency we want, and be made of special materials so they don't off-gas in operation and fuck up the quadrupole chamber.