by
lmh » Thu Dec 15, 2016 2:31 pm
I'd reiterate, the main reason for not doing it is merely that it's generally pointless.
There is an optimum flow-rate for a column (van Deemter plots and all that). Ideally, for best resolution, you would run your column at the minimum of the van Deemter plot. Often this isn't achievable because the minimum happens at too high a back-pressure, or (opposite situation) you want a shorter method and you're prepared to sacrifice some resolution by running faster.
You can't improve separation by changing the flow-rate (unless you're working at a really silly flow-rate, in which case why are you working at that flow rate at all?). Flow-rate isn't the same as concentration. You change the concentration of the solvent in order to change the degree to which the analyte is retained, and you need to do this if you're looking at two wildly-different analytes (as you are! One is barely retained, so you might not want to use 95% ACN at that stage). Changing the flow rate has two effects: it stretches/compresses the time-axis, and it gives more/less time for diffusion effects in the column, which means it influences peak-width. That's all it does.
If you are running at less than the optimal flow-rate, then speeding up is a good idea if you can. If you are running at the optimal flow-rate, then slowing down is always a bad idea (unless you are obliged to for non-chromatographic reasons, like a very slow detector). If you have enormous separation between peaks, then slowing down is pointless. If you're worried about the separation between your injection peak and your first analyte peak, then changing solvent composition will give you better retention, while, if you're working at a relatively flat bit of the van Deemter curve, or you're already at the optimum, slowing down will either not affect, or will harm, resolution (even if it increases the distance between the peaks).
There are useful applications for increasing flow, for example speeding up washes and re-equilibrations.
The issue of it affecting peak area is only relevant if you're trying to compare peaks at one retention time with peaks at another. If you're calibrating each peak against a standard, or you're comparing the same peak between multiple samples, it will have eluted under the same flow conditions.
You wrote about changing flow as a chromatographic no-no. There are a handful of situations where it really is a no-no. For example, to run a method fast until peak 1 has eluted, slow the flow, and then speed it up again just before peak 2 elutes, is definitely bad practice, to the point of fraud. It makes it look as though the selectivity of the method is much higher than it really is.