In this customer interview, we have invited Anatoliy Trokhymchuk and Mengying Liu from the Animal Health Laboratory. They will share with us their use of the Opentrons OT-2 automated pipetting platform for mass spectrometry applications including MALDI-TOF MS target preparation.
Anatoliy Trokhymchuk is Prairie Diagnostic Services Inc. (PDS), a regional animal health laboratory affiliated with the University of Saskatchewan. Mengying Liu is a PDS process improvement and automated workflow Developed by Automation Researcher. One of her automation development cases is the use of Opentrons OT-2 automated pipetting platform for mass spectrometry applications, including MALDI -TOF MS target preparation.
Opentrons: Please introduce your research background.
Mengying Liu: I am a research assistant at PDS. I received my doctorate in veterinary medicine from China Agricultural University and then came to the University of Saskatchewan to pursue my master's degree in veterinary pathology. I started working for PDS at the end of January. I am interested in computer programming and combining it with laboratory testing, I enjoyed my time at PDS.
Opentrons: What are your research projects?
Anatoliy Trokhymchuk: I am a veterinarian working for a regional veterinary diagnostic laboratory and my daily work involves dealing with a variety of clients and projects. Some projects, such as surveillance testing and outbreak response, require large-scale testing efforts. We have a great group of talented people at PDS and it’s my job to inspire them and provide them with the necessary support they need to have the tools they need to do their job.
Opentrons: Why did you choose OT-2?
Anatoliy Trokhymchuk: As our workload increases and diagnostic methods change, we need to complete more and more precise routine and repetitive tasks in the laboratory. We gradually realize that automation is the experiment room future trends. We already have many different types of robots in our lab, and we are quickly learning how to use the OT-2. In the near future, we will have more rapid genome-based diagnostics, and automation is an important part of completing these tasks.
I think the main goal of humans in the laboratory is to explore the boundaries of science and constantly try scientific innovations. – Mengying Liu
Opentrons: What projects have you done using the OT-2, and how does it fit into your workflow?
Anatoliy Trokhymchuk: Currently, OT-2 has two main uses in our laboratory: one is to run the automated process Mengying is using, and the other is as a learning tool. We are learning how to optimize protocols and improve work output to grow our business. We like OT-2 very much as a research tool, but we also like the greater exploration value it brings: How can we automate larger tasks and integrate them into our workflow?
Opentrons: What is your daily routine like in the lab? What detection methods will you use?
Mengying Liu: My day-to-day work is devoted to the development and operation of automated processes for different laboratory tests, such as MALDI target coating. Our system uses a manufacturer-independent 96-point target. I created a workflow and protocol using the OT-2 automated pipetting platform in our lab.
Before we had the OT-2, our operators had to manually drop the matrix into the 96 wells, and the bacterial sample was already sampled on the target when doing this step. This job can easily be replaced by robots. Additionally, because we are a diagnostic laboratory, we must ensure there is no sample contamination, so operators need to change tips every time they operate. The OT-2 can accurately handle pipettes down to 0.1 mm, allowing us to drop-dose matrix without touching the sample – we only needed to use 8 pipette tips for the entire target, reducing plastic waste.
The laboratory is not a place to waste time on pipetting all day, experimental work needs to be productive and creative. – Anatoliy Trokhymchuk
Furthermore, the protocol we designed is easy to set up. That's why we use the OT-2: A skilled technician can perform the entire workflow manually in 5 minutes, and the OT-2 can do it roughly the same speed. But the advantage of the OT-2 is that it doesn’t require a highly skilled technician to perform the same process, which frees up the technician’s time to do other things. We are working to standardize this across the laboratory.
I linked the OT-2 to our LIMS system by using the Opentrons API and a custom interface to generate plate plots showing controls and samples, which I could export to a plain text file and upload as my protocol. This saves a lot of time and allows for easy integration with other tools in the lab. The OT-2 is easy to use as I only have to calibrate the robot once at the beginning and can perform up to 8 boards at a time. I am exploring other applications for the OT-2 to make it easier to incorporate into work in other labs.
The OT-2 has different integration potential, so when the MALDI workflow is completed, I will use it for other workflows.
Opentrons: What was your normal daily routine before the pandemic?
Anatoliy Trokhymchuk: The daily work we are doing now is exactly the same as before the epidemic. However, during this pandemic, we are required to wear masks in the laboratory and follow all precautions prescribed by public health authorities. We consider our services to be essential, and although we do not know the extent of the outbreak here or whether our laboratories will be called upon to provide testing support, our functions and work have not changed. We are not directly involved in the outbreak response, but our counterparts in the Canadian province of Quebec are using their animal health laboratories for COVID-19 testing.
Opentrons: Do you have any other automation projects planned?
Anatoliy Trokhymchuk: I would like to see all the automation tools in our lab work together seamlessly, and then I could offload a lot of the routine lab tasks to the robots while we technicians take care of it. Process supervision, control and development applications. The laboratory is not a place to waste time on pipetting all day, experimental work needs to be productive and creative.
Mengying Liu: That is also the future I sincerely hope to see! I believe that one day all these repetitive tasks will be replaced by automation. I think the main goal of humans in the laboratory is to explore the boundaries of science and constantly try scientific innovations. Rather than spending time on repetitive work, we should do more experimental and innovative projects.
Opentrons: Is there anything else you would like to share with everyone about your experience using OT-2?
Anatoliy Trokhymchuk: Regarding experimental workflow design, we still have a lot to learn, not just automation. This is a gradual process. We are learning step by step and prioritizing major projects. Ultimately, handing over the entire workflow to a robotics platform is a great idea, but I think we're still very far away. Nevertheless, due to the unique flexibility and open source characteristics of Opentrons, it provides us with the opportunity to move towards full-process automation.
Mengying Liu: I really like the flexibility of the OT-2. Some companies only design machines for MALDI, but we can do a lot of different protocols on the OT-2.
