Hi Matthew,
I'll definitely defer to Adeeb, Zach, and a bunch of other people who often do long barcoding runs, but here are some general guidelines:
1. I personally have not found it necessary to clean the cones during long runs (ie, shut down, remove them, sonicate or use Brasso, rinse, then reinsert). This mostly affects the Current setting, where I haven't seen much drift even over the course of a week as long as samples are well washed in MilliQ to remove residual salt.
2. If I am doing long runs (>6hr), I typically stop, clean with Wash, then rerun Tuning (then Wash to remove Tuning and then MilliQ rinse, of course). The time interval depends a bit: I'd guess every 4 hr is probably sufficient, based on my experience. So, if you're doing an 8hr run, stop at the 4hr mark, retune, and then resume. You can shift that time interval a bit as needed: for example, if you have a 9hr run, I would retune at 4.5hr and be done with it, rather than at 4hr, then 8hr. If you have a 10hr run, I would probably do 3.5hr, 7hr; or just one at 5hr.
-Some of this will depend on the instrument model you have: A Helios drifts a lot less than a v1, and I think less than a v2.
-While you can certainly retune as often as you want, I don't think you'll see a benefit retuning any more frequently than every 4hr or so. And, at ~15min/retune + 10min or so Washing before and after, you're approaching 30min per Retune.
3. It is critical that you redo Mass Calibration, Dual Slopes, and Detector Voltage when you retune. Those are the main things that will drift. On a Helios, there is usually a Quick Tune Protocol that basically covers those things; however, I've seldom been able to get it to work properly.....therefore, I just do the whole Full Protocol which takes about 15min.
4. If you are running a barcoded sample, 4hr may be one sample or multiple samples. Since MilliQ water is so harsh even on fixed cells, samples are usually more stable as cell pellets with minimal overlay (resuspend and filter just before putting on the machine). Therefore, it is often a good idea to split one giant BC sample into a few smaller pellet aliquots. Here's a thread on the topic:
viewtopic.php?f=3&t=671&p=2260&hilit=normalization#p2260- this does not inherently mean you have to run them as separate files (though you may wish to); you can always add in the next aliquot to the sampling tube on the fly.
Mike