It’s funny. Every time I discuss about protein purification with someone I realize that there are extremely efficient ways to waste all your precious material in seconds, just because of distraction, lack of experience, or untrustable colleagues. And it seems that “becoming experienced” on the Akta means wasting bucketfuls of proteins from time to time.
So, I decided to prepare this “Top 5 reasons of failed protein purification using the Akta system” post and I hope that will help newbies to save their protein during their next purifications. Let’s start:
Unwanted air in the system that masks your protein peaks
Ok. Everybody knows that air and Akta are not compatible, but how many times a non-experienced user lets air inside the system? Sometimes people think that it’s just the column that should be kept free of air, but this is absolutely not true. An example: a 100 microliters loop left in “load” mode without syringe for a few seconds will introduce enough air in a MonoQ 5/50 column to generate annoying air spikes for the next 10 column volumes. Can you imagine the amount of air that can be introduced in a system just by changing a connection tube before or after your column, or replacing a loop?
Before your run, ensure you connected all your tubings and loops to the system. Bypass the column with a connector (the system should be “closed”) and flush the system with your buffer for at least 5-10 mls (should be enough to rinse all tubings from pumps to fraction collectors on most akta systems) with a high flow-rate (5-10 ml/min, unless you have special setups that require lower flow-rates, check your system!!!). The high flow-rate is required to remove occasional air bubbles trapped in the connectors or in the detector cell.
The sudden “after pumpwash” elution
One of the most horrible ways to lose your protein is see it coming out when you don’t expect it, and the Akta actually does not really help in avoiding it. The typical scenario is the following: IMAC, batch binding of a protein sample and manual packing of a column, you connect it to the Akta, your buffers A and B are on pumps A and B. Pumpwash, then start washing your column with buffer A, to remove non-specific contaminants before the elution with buffer B. Wait, that peak is too high, it’s really strange… anyway, let’s keep going, the UV signal is now flat, let’s do the elution with B… How come? there’s no peak! where’s my protein? Noooooooooo!!!!!! What happened?
Actually, I consider this a “bug” of the akta system: it depends on the dead volumes between pumps and valves. When you do a pumpwash, doesn’t matter which pump you will be using afterwards, the first 2-3 ml that will pass through the system (and through your column, if it’s connected) will be a mixture of your buffers A and B, which remains in the injection valve after the end of the pumpwash. If you are working with a 1 ml column (IMAC, MonoQ/S or something else), this tiny volume of concentrated elution buffer will elute all your sample, together with the damn contaminants, at the very beginning of your run. To avoid this unpleasant event, put your buffers on the Akta and wash the pumps before connecting your columns, or if your really need to swap your buffers during the run while your sample has already been applied to the column, disconnect (bypass) the column and flush the whole system for 5-10 ml after a pumpwash, and reconnect the column only after this step.
The mistery of the partial filling of the sample loop
I injected 500 micrograms of protein in 1 ml sample using a 1 ml loop, but I recovered only 300 micrograms… why?
This picture (taken from GE website) shows what happens to your sample when you apply it to a sample loop. Partial filling is the most efficient way to ensure 100% sample recovery using loops for injection.
Assuming that you really injected 500 micrograms of protein, that the sample did not stick to the plastic of the syringe, to the tubings or to the column beads, it may well be that you lost part of the sample because you sent it to the waste while filling the loop. Liquids actually do not migrate as straight lines in the akta tubes, and the more a tubing is narrow, the more the liquid will be retained by the inner surface of the tubing. That’s why partial filling of sample loops is the best way to ensure complete recovery of your sample during a run on the Akta. If you have a sample volume of 1 ml, use a 2 ml loop, and after applying your sample to the loop leave the system in inject mode for at least 3-5 times the volume of the loop (in the case of a 2 ml loop, use 10 ml). In many cases, you can leave the system in inject mode for the whole elution procedure (unless you need to use the sample valve for other reasons).
Loop bypass: from a syringe to the waste
Ok, we just discussed the partial filling of the sample loop, we are sure that there is no air in the system and the loop has been rinsed properly, by flushing it with a syringe from the injection port. To avoid the introduction of air in the loop, the wash syringe is still connected. So, the system is running, the column is connected, to remove my syringe from the injection port the system needs to be switched to inject mode, then I pick my sample, put the syringe in the injection port and push the plunger… The column is running, but nothing is coming out.
In load mode, the sample loop is connected to the injection port, which cannot be left open. In inject mode, the injection port is directly connected to the waste and the sample loop is bypassed.
Yes, it’s horrible to realize that your samples has never been injected in the column, because you forgot to switch to load before pushing the plunger of your sample syringe. In Inject mode, the injection port is connected directly to the waste, and the sample loop is completely bypassed. The correct procedure is the following: (1) while the system is in load, wash the sample loop using a syringe with a volume capacity larger than the loop itself. (2) when it’s time to apply your sample, switch to inject, remove your wash syringe and put the sample syringe in the injection port, but do not push the plunger. (3) switch the system to load, and push the plunger of your sample syringe: your sample will go inside the loop. (4) switch the system again to inject to apply the sample to your column.
What if your colleague left a dirty column?
Your colleagues can be good friends, comrades, very helpul collaborators and will keep the spirit up during your daily life. However, you cannot trust everyone in everything, in particular when it regards doing cleanups or boring washing procedures. This means that, the more a column requires cleaning, the more you will find it dirty when you will really need it. And it will be horrible to see your protein on an SDS gel with additional bands of dirt after column processing (and trust me, it happens…)
So, if you are processing the sample of your life, do not trust your colleagues, do not trust your friends, do not trust your technicians. Wash your columns throughly before your run and make sure that they are properly clean when your sample will be applied.