Anatoliy Trokhymchuk is the Chief Scientific Officer for Prairie Diagnostic Services Inc. (PDS), a regional animal health lab associated with University of Saskatchewan. Mengying Liu is an automation research associate at PDS handling process improvement and automated workflow development. One of the examples is mass spectrometry applications including MALDI-TOF MS target preparation using an Opentrons OT-2 liquid handling robot. Here’s how.
Opentrons: Tell us about your background.
Mengying Liu: I’m a research associate working at PDS. I received my DVM degree at China Agricultural University and came to University of Saskatchewan to get my master’s degree in veterinary pathology. I started working for PDS right at the end of January. I’m interested in computer programming and combining it with laboratory assays, and I’m enjoying learning at PDS.
Opentrons: What kind of research do you do?
Anatoliy Trokhymchuk: I’m a veterinarian working for a regional diagnostic lab, dealing with a variety of clients and objectives. Some objectives, like surveillance testing and outbreak response, require really large scale testing. We have a good group of people at PDS, and it’s my job to cheerlead and make sure they have all the tools they need to get their jobs done.
Opentrons: Why did you choose the OT-2?
Anatoliy Trokhymchuk: With increased work volumes and changing diagnostic methods, we needed more—and more highly accurate—routine, repetitive tasks done in the lab, and we realized automation is the way to go. We already had many different kinds of robots in the lab, and we are learning the OT-2 quickly. There will be more genomics-based rapid diagnostics happening in the near future, and automation is a big part of them.
I think the main goal of human beings in the lab is to explore the edges of science and see what innovations we can make. - Mengying Liu
Opentrons: What specifically do you use the OT-2 to do, and how does it fit into your workflows?
Anatoliy Trokhymchuk: There are two parts to the answer: one is the protocols Mengying is using, and the other is using the OT-2 as a learning tool. We’re really learning how we can optimize protocols and workload to scale our operations. We really like the OT-2 as a tool, but we like it better in a bigger context: how do we automate bigger tasks and integrate it into our workflow?
Opentrons: What’s a typical day in the lab for you? What assays do you use?
Mengying Liu: I work on automation of different laboratory assays—one example is MALDI target coating. Our system uses a 96 spot target and is manufacturer agnostic. I created a workflow and protocol for the application in our lab using the OT-2 liquid handling robot.
Before we had the OT-2, a technician had to pipette matrix onto the well 96 times by hand after the bacteria was sampled onto the target, which could easily be replaced by the robot. Also, because we are a diagnostic lab, we have to make sure there’s no sample contamination, so a technician has to change the pipette tip every time. The OT-2 can precisely handle pipetting to 0.1 mm, which allows us to dispense the matrix without touching samples in the well—and we only need 8 tips for a whole target, reducing plastic waste.
The lab isn’t a place to grind at a pipette all day long, but to be productive and creative. – Anatoliy Trokhymchuk
Moreover, the protocol we designed can be set up easily. That’s why we use the OT-2: a skilled technician can manually pipette the protocol in 5 minutes, but the OT-2 can do it roughly that quickly, too. But the benefit is not needing a highly skilled tech—and freeing that tech’s time to do something else. We are working to standardize this throughout the lab.
Using the Opentrons API and a customized interface, I linked the robot to our LIMS system to generate a plate map showing where the controls and samples are, which I can export as a plain text file and upload as my protocol. It saves a lot of time, and integrates easily with our other tools in the lab. It’s easy to do with the OT-2 because I just need to calibrate the robot once at the beginning and it can do up to 8 plates each time. I’m exploring other applications of the OT-2 to make other lab work easier as well.
The OT-2 has potential for different integrations, so when I’m finished with the MALDI workflow I will use it for other workflows.
Opentrons: What was your normal day-to-day routine before the pandemic?
Anatoliy Trokhymchuk: Prior to the pandemic, our routine was exactly the same. However, during the pandemic we are required to wear masks in the lab and follow all the precautions prescribed by public health authorities. We’re considered essential service, and our function and work hasn’t changed, even though there was a brief tense moment when we didn’t know how bad the outbreak would be here in Western Canada and if our lab would be called on to help respond. We were not directly involved in the pandemic response, but our counterparts in Quebec were and their animal health lab was repurposed for COVID-19 testing.
Opentrons: Are you planning any other automation?
Anatoliy Trokhymchuk: I’d like to see all the automation tools in our lab working seamlessly together, mundane lab tasks given to the robot, and humans give oversight, control, and develop applications. The lab isn’t a place to grind at a pipette all day long, but to be productive and creative.
Mengying Liu: That would be a future I would really like to see! I believe one day all of this repetitive work will be replaced by automation. I think the main goal of human beings in the lab is to explore the edges of science and see what innovations we can make. No repetitive work involved, but more experimental-type things.
Opentrons: Is there anything else you’d like to say about using the OT-2?
Anatoliy Trokhymchuk: There’s still a lot to learn about workflow design, not just automation. It’s a gradual process. We’re learning one step at a time, and targeting primary tasks first. Eventually, it would be nice to hand off entire workflows to robotic platforms, but I think we’re quite a ways away from that. Still, automation offers us the opportunity to do just that because of the flexibility and nature of the platform.
Mengying Liu: I really like the flexibility of the OT-2. There are some companies that design machines only for MALDI, but we can do a lot of different protocols on the OT-2.
Header photo credit: Government of Saskatchewan.