HPLC Mobile Phases: acetonitrile vs methanol. Which one is better?

What is the difference between methanol and acetonitrile?

If you are doing HPLC then you need a mobile phase. It plays a key role in the separation. The mobile phase dissolves the sample and carries it through the column. That is the job of the mobile phase.

Now there is actually competition for the analyte between the stationary phase and the mobile phase. The stationary phase tries to hold on to your molecule and the mobile phase tries to pull it off the column.

So the mobile phase plays a pretty important and active role in the separation process.

In the LC world we have a number of choices for the mobile phase, but practically it comes down to methanol and acetonitrile. The third choice is THF, tetrahydrofuran - not really popular.

So most of us out there are using methanol and acetonitrile. And, a lot of people ask, “What’s the difference?”

Well, I’ll give you a couple of answers - and the first statement is gonna sound a little non-scientific.

Eh - they are pretty much the same.

Now, they are not the same. They have different chemistries and different properties. But they are very similar.

Here is the way I put it: If you have something that works with acetonitrile as the mobile phase, then you have about a 85% chance that it will work with methanol as the mobile phase.

And vice versa ,if you have something that works with methanol, then you have about a 85% chance that it will work with acetonitrile.

I won’t say that they are interchangeable in all scenarios because they do have different chemistries.

Since there isn’t a huge performance difference, choose one that makes sense and is convenient for you.

For example, If you have 9 methods running methanol as the mobile phase and you need to develop a tenth method, please try methanol!

In the grand scheme of things - and if you were going to twist my arm and say ‘which one is better?” - I would have to admit that acetonitrile is a little better.

Why is acetonitrile a better solvent?

Acetonitrile is a slightly stronger solvent than methanol. It is a little cleaner in the UV; you can go all the way down to 190 nanometers with acetonitrile (versus 210 nanometers for methanol). Acetonitrile has a little lower viscosity therefore requires less pressure. For those reasons acetonitrile is a little better than methanol - if price is not an issue.

Why is methanol better?

But if price is an issue then acetonitrile is more expensive. In 2008 the price of acetonitrile skyrocketed and never came all the way back down.

Here in my lab I usually use methanol; that is my primary choice.


And then if methanol doesn't work then I will switch to acetonitrile. I like that approach because methanol is cheaper and it's also perceived to be a little less toxic. I'm not sure if that's true - I don't claim to be a health expert but consider this: the official IUPAC name for acetonitrile is methyl cyanide. So people are a little worried about having giant boxes of methyl cyanide sitting around the lab versus methanol. Now from my perspective they're both poisonous - don't drink either of them! Don't drink your mobile phase if that's the take away from this.

So methanol and acetonitrile - they're both great. Acetonitrile is slightly better. Methanol is a lot cheaper. So my approach nowadays is use methanol and when it doesn't work try acetonitrile it's perfectly valid to take the other approach: use acetonitrile and if it doesn't work then try methanol.

I hope that helps sort it out a little bit. If you want to know more information, come take one of the classes because we really have to get into the nitty-gritty of something we call resolution and how that methanol actually dissolves things versus the acetonitrile. So lots more fun stuff to learn and thanks for stopping by.