Chromatography Forum

Does anyone have any guidance they can pass on as to how to set the fragmentor on an 1100MSD? Is there some rule of thumb (ie., 70 to avoid fragmentation, 150 to enhance) that you use for new compounds, or is it strictly experimentally determined? I've played around with it, but in reality can't see much difference in the settings. Also, how do you determine the applied voltage? Do you just assume 4500V, or, again, is there some rule of thumb you use to set the capillary voltage? I'm running small polar compounds (pesticides) using 0.1% HAc/acetonitrile.

For the spray voltage, I'd recommend Agilent's defaults.

The fragmentor voltage does make a difference, but if you're doing SIM for target molecules and you're not working near the detection limit, you probably won't notice the difference, or need to worry about it.

If you want to see the difference, make a standard mix containing a range of your favourite analytes, and do flow injection analysis (which makes multiple injections at intervals during a single "chromatography" run), with no column, but some sort of resistance instead (back-pressure regulator or 1m of thin tubing). Use full scan data, and extract ion chromatograms for each component of your standard mix. This will give you a series of "peaks". You can set up flow injection analysis to make each injection after changing the fragmentor voltage. You'll see how the peaks (in extracted ion chromatograms for each target mass) get larger as the voltage increases, and then shrink again, and the effect is very mass-dependent.

Heavy ions take more fragmentor voltage to get them into the instrument. Light ions need less. But I'm afraid there is no rule of thumb, it is compound dependent, because the limiting factor is fragmentation, which depends on the delicacy of the ion. If you use too high a voltage, the ion will fragment, and you will lose intensity of the parent ion that you've presumably chosen for SIM, and for extracted ion chromatograms, as the parent is converted to fragments.

I used (and use) 70V a lot, but it's nowhere near enough to get big ions into the detector. By mass 1000 it's hopelessly low.

My personal favourite compromise voltage for a set of standards based on flavonoids and sugars is 140V, and as a ramp, I'd suggest 100V up to about mass 200, then ramping up to about 370V by 1200, and holding this voltage thereafter. For maltoheptaose, mass 1175, the unfragmented parent dominates even at 400V.

Of course to some extent these voltages are also dependent on your instrument and your chosen spray-chamber conditions, because as I understand it, they are applied at a stage of the instrument where the level of vacuum will still depend a little on how efficiently you're drying off all the solvent, and both the voltage needed to drag something into the instrument, and the voltage you can get away with before fragmentation, do depend on the gas pressure of the region through which you're dragging the ion.

Which is another reason why it's probably worth doing the flow injection analysis! Good luck!