You can use freeze-dryers to dry, store, and buffer exchange samples. Avoid using organic solvents, ensure samples are fully frozen, and release the vacuum gently. Regularly thaw and drain the chiller and change the vacuum pump oil when it runs low or becomes contaminated. Ensure the vacuum tubing is firmly attached to the instrument and pump to prevent vacuum leaks. Troubleshoot vacuum leaks using the checklist below, but don’t disassemble the instrument if it’s under warranty.

I used to work as a technician in a lab where the freeze dryers were essential and continually in use. The researchers used them to dry everything from nanoparticles and DNA to eggshells and shellfish. 

When it broke down, which it inevitably did, it harmed people’s research and productivity.  

To reduce the frequency of freeze dryer breakdowns in your lab, here are some essential tips for using and maintaining your lab’s freeze dryer, including changing the vacuum pump oil and troubleshooting vacuum leaks. 

What Can You Use a Freeze Dryer For?

If you’re unfamiliar with freeze dryers and what they can do, here are some handy things you can use them for: 

  • Drying DNA if, for example, your miniprep products are too dilute.
  • Drying hygroscopic lab reagents that have become wet.
  • Drying plants and fungi for long-term storage. 
  • Drying protein samples. 
  • Removing the water from nanoparticle suspensions. 
  • Freeze-drying your leftover lunch for a later date (just kidding).

You can use them whenever you need to remove water from a sample, provided it can tolerate the drying process. The end goal is usually sample dehydration, storage, or buffer exchange, where you dry a sample and reconstitute it in a different buffer system.  

How a Freeze Dryer Works 

To maintain your freeze dryer, it’s helpful to understand how it works and what each component does.

Ice sublimes in a vacuum at low temperatures. It turns from a solid (ice) into a gas (water vapor) without ever existing as a liquid (water) during the transition. 

During freeze drying, samples are frozen and placed in a cold chamber from which all the air is removed to create a vacuum. The ice in the sample sublimes and the water vapor is drawn over a chiller. The water vapor turns back to ice on the chiller, and eventually, almost all the water initially in the sample gets transferred from your sample to the chiller, thus drying it. Everything in your sample but the water is left where it started.

To freeze your samples, you can either immerse them in liquid nitrogen or place them in your lab freezer until fully frozen. Ensure whatever container your sample is stored in has a few small holes in it for the water vapor to escape through. Hypodermic needles are great for punching holes in the lids of Falcon™ tubes and other lab plasticware.

Note that it’s more technically accurate to say that samples are cooled below the triple point of water, 0.01°C, which is the temperature and pressure at which water vapor, liquid water, and ice can all coexist. This ensures the sublimation rather than the melting of the ice in your sample.

The Anatomy of a Freeze Dryer

There are two types of freeze dryers you are likely to encounter in the lab:

  1. Cabinet freeze dryers. 
  2. Manifold freeze dryers. 

Cabinet freeze dryers resemble lab ovens, shaped like a box with hinged doors that open onto the vacuum chamber that’s arranged like a kitchen cabinet (hence the name).

Manifold freeze dryers have a vacuum chamber reminiscent of a bell jar that rests on top of the chiller/control unit. It’s held in place by the vacuum when the pump is switched on but otherwise lifts on and off the chiller with nothing to hold it in place.

Often, the vacuum chamber has manifolds (hence the name) attached to the rim of the vacuum chamber to which you can attach smaller sample holders. 

Figure 1 (below) shows a pair of manifold freeze dryers.


Tips for Using and Maintaining Your Laboratory's Freeze Dryer
Figure 1. A pair of manifold freeze dryers (Image credit: Thomas Warwick.)

Here’s a short description of the main components of a freeze dryer and their purpose.

1. Vacuum Pump

Vacuum pumps create the vacuum needed for ice to sublime. Most vacuum pumps in the lab are rotary vane pumps and pull vacuums in the low milliTorr/microTorr range. The pump is connected to the chiller/control unit with vacuum tubing.

2. Chiller 

The chiller is a polished stainless steel dish inside the control unit that collects the sublimated ice from the sample. Vacuum tubing from the pump connects to the chiller, usually at the back. The chiller also features a drainage system to remove ice build-up.

Note also that the chiller is kept at a temperature below that of your samples to collect the sublimated ice from them.

3. Control Unit

The control unit houses the internal electronics that make the freezer dryer work and insulation packed around the outside of the chiller. 

A control panel on the front allows users to switch the vacuum on and off, prepare and run specific freeze-drying programs, and monitor the vacuum and temperature inside the vacuum chamber. 

A big “start/stop” button toggles between freeze drying and idle states, and on many models, the pump remains inactive while the temperature of the chiller and vacuum chamber is cooled to below 0 °C. At this point, the pump kicks in and begins to pull a vacuum. The result is a slight delay between pushing “start/stop” and the pump kicking in.

4. Vacuum Chamber

The vacuum chamber houses your frozen samples. It’s typically made of clear, durable plastic and has a rubber O-ring around its bottom rim that forms a seal when the chamber is resting on top of the chiller/control unit. 

As mentioned above, the vacuum chamber may have ports to which you can attach smaller sample holders. It may also have a central drying rack on which to rest samples. There are also sensors to monitor the temperature and pressure of the system.

5. Vacuum Tubing

The vacuum tubing connects the pump to the chiller/control unit and the vacuum chamber. It’s usually made of a durable, insulated rubber and comes in various lengths and diameters. 

Freeze Drying and Instrument Maintenance Tips

While freeze-drying samples is an easy process, there are steps you can take to ensure they are freeze-dried efficiently and to help maintain your lab’s freeze-dryer.

Ensure Your Samples Are Free of Organic Solvents

Don’t freeze-dry anything containing organic solvents. Some organic solvents may freeze and sublime along with the water in your sample, while others may remain unfrozen when you freeze your bulk sample, and unfrozen solvents will boil (turn from a liquid to gas) when under a vacuum.

Either way, the organic solvent vapors can damage the components of the freeze dryer, eating away at the rubber and plastic and causing irreparable damage.

Ensure Your Samples are Fully Frozen

Ensure samples are fully frozen before attempting to freeze-dry them. Unfrozen water will boil, potentially mechanically and chemically damaging your sample. 

Release the Vacuum Gently

Release the vacuum gently when retrieving samples. Air rushing to fill the vacuum can be turbulent, causing samples to move. Powdered samples might get blown around and contaminate others, while fragile samples might get smashed. 

Drain the Chiller Regularly

Periodically thaw the ice and drain the water from the chiller to ensure that your samples freeze dry efficiently. If you have samples resting on some cork inside the dish of the chiller, they can become entombed in ice if it is allowed to build up.

Don’t Leave the Pump Running If the System Is Open to Air

Don’t leave the pump running if there is an open valve. This will let air in and overwork the pump, causing the vacuum pump oil to burn off, eventually damaging the pump. Plus, if you have a frozen sample on the instrument, it will defrost.

The pump will usually make a louder noise than usual if there is an open valve and there won’t be a vacuum. If you can’t hear air hissing through any valves, put the palm of your hand over each one in turn and feel for suction. 

Troubleshooting Vacuum Issues

Anyone who uses a freeze dryer regularly will encounter a situation where the instrument fails to pull a sufficient vacuum to freeze dry samples. In my experience, this threshold is around 15–30 milliTorr, but this will depend on your specific instrument and its operating parameters. 

Troubleshooting vacuum leaks can be a pain because the gap causing the leak can be tiny and difficult to locate. 

The best way to troubleshoot vacuum leaks is to start with the obvious, replaceable items and eliminate them first. Here’s a checklist of what to do.


Vacuum Troubleshooting Checklist

The best thing to do first is a quick sanity check to see if there is genuinely a vacuum leak. Faulty vacuum sensors may return vacuum readings that suggest a vacuum leak when there isn’t one. 

You could hook an analog vacuum gauge up to the instrument while the pump is running and check to see if the vacuum reading matches the digital readout on the instrument.

Or you could simply freeze dry some tap water and see if the ice sublimes. Even if there is a leak, you might find it’s small enough not to inhibit the freeze-drying process. Just note that small leaks will probably worsen over time.

If you’re confident there is a leak, you can skip those steps.

Check the sample containers, manifolds, and valves to ensure nothing has accidentally been left open.

Ensure no one else has recently put a frozen sample on the instrument. Sublimation from recently added samples will temporarily increase the pressure on the instrument.

Check the gaskets and O-rings that seal the sample containers to the manifolds attached to the central vacuum chamber. Sometimes these get dislodged or fall out.

Check all other gaskets and O-rings. Ensure no dirt or grit on them could break the vacuum seal. Clean and dry them if they look dirty. You could also try applying a minimal amount of vacuum grease to them.

Thaw and drain the chiller unit of any ice. If there is a lot of ice build-up in the chiller, it could block the hole where the pump is attached.

Change the vacuum pump oil (see below).

Check the external vacuum tubing for damage, especially where it connects to the pump or the control unit. The vacuum tubing usually slides over an inch or so of metal to give it some purchase. However, these bits of metal can puncture through the tubing over time as the rubber becomes brittle.

Finally, unplug the instrument, remove the side panels, and check the internal vacuum tubing for damage and tears. There’s often a length of tubing that runs from the back of the electronic control panel to the rear of the instrument, which can perish over time.

If your instrument is under warranty or a service contract—don’t disassemble it to search for internal leaks. This will probably void your contract!

Instead, call the service engineer after you’ve eliminated all the obvious possible sources of the leak. For the rest of us, if you suspect a leak in the vacuum tubing, then jubilee clips and tie wraps/zip ties are your friends. Sometimes, you can eliminate leaks caused by loose tubing by attaching them where the vacuum tubing connects to the pump or the chiller/control unit to cinch any gaps.

You can also cut off frayed and damaged vacuum tubing. Most damage will occur at the end of the tubing or where it’s stretched or bent. If you need to cut the vacuum tubing, use a tool with a sharp blade to make a neat cut. Stanley knives work great.

If the leak is in the middle of the tubing, or cutting off the ends of the tubing won’t leave you with enough left, you will have to order some replacement tubing.

The three parameters you need to know to order new tubing are:

1. Its length.
2. Its internal diameter.
3. Its external diameter.

Unless you have the instrument specifications, you will have to guesstimate the last two parameters. Try to estimate the internal diameter accurately (within a millimeter). Too large, and the tubing will be too baggy to pull a vacuum; too small, and you won’t be able to slide it onto the pump or chiller/control unit.


How Often Should You Change the Vacuum Pump Oil? 

Vacuum pump oil is essential for the pump to pull a vacuum. It also cools and lubricates the pump while capturing contaminants.

However, it burns off over time (and gets increasingly contaminated), so it needs to be changed periodically. Change the pump oil if:

  • The freeze dryer isn’t pulling its usual vacuum;
  • You know or suspect the oil is contaminated;
  • When the oil drops below the minimum required level indicated on the pump.

How to Change the Vacuum Pump Oil

Turn the pump off at the mains and via the rocker switch on the pump. 

Allow the pump to cool down. You might have to leave the pump overnight if it is a large one. 

Disconnect the vacuum tubing from the pump, and be careful not to lose any clips and gaskets.

Locate and unscrew the oil reservoir cap, where you top the pump up with new oil. It’s usually on top of the pump and about the size of a bath plug (Figure 2).

Locate the oil drainage cap on the pump. It’s usually located on the front of the pump (Figure 2).


Tips for Using and Maintaining Your Laboratory's Freeze Dryer
Figure 2. A pair of vacuum pumps (Image credit: Thomas Warwick.)

Unscrew the drainage cap and tip out the old oil into a plastic container. Flush out residual oil with some new vacuum oil. 

Screw the drainage cap back in, then fill up the pump with fresh oil. The pump should have an oil-level indicator with the maximum oil level marked on it. 

When you have filled the pump with oil, screw the reservoir cap back in. 

Reattach the vacuum tubing to the pump, and ensure it’s correctly in position and clamped tight to prevent leaks. 

Plug the pump back into the wall and switch it on at the mains. Switch it on at the rocker switch on the pump, then proceed to check that it’s pulling a vacuum. 

Sign out the used oil as vacuum oil waste or label it and store it in your lab until dedicated personnel dispose of it. 

Some vacuum pumps are quite heavy (10–20Kg). Heavy pumps usually live on the floor and need lifting onto a surface to drain. When this is the case, ask someone to help you lift it onto a lab bench so that the drainage plug is hanging over the edge, but the pump will not fall. Then, place a bowl on the floor and carefully tilt the vacuum pump so that the oil leaks out and falls into the bowl.

Don’t drop it on your foot. 

Freeze Dryer Use and Care in Summary

Those are your essential freeze dryer usage and maintenance tips. Avoid organic solvents, change the pump oil every so often, and keep an eye out for vacuum leaks. 

Should you notice a vacuum leak, call out the engineer or work through the above checklist if you feel confident enough. 

And if I’ve left anything out or you have additional advice, let me know in the comments section below. 

For more helpful information on looking after your lab equipment, visit Bitesize Bio’s Lab DIY Hub. 

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