Opentrons Customer Interview | Scott Ficarro, Dana-Farber Cancer Institute

Opentrons' Kristin Ellis and Dagney Cooke had the pleasure of speaking with Scott Ficarro at the Dana-Farber Cancer Institute (DFCI) in Boston. Scott, a research scientist in the Marto lab, Division of Cancer Biology, and Blais Center for Proteomics, has been using OT-1 for large-scale sample preparation.

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Kristin: First, we would like to understand the overall picture of the research you are conducting and what role our platform plays in this process.

Scott: Okay! We are conducting many experiments related to sample preparation for mass spectrometry experiments with OT-1. This involves many different possibilities, from digestion to phosphopeptide enrichment and more.

Kristin: Is this what you hope to do with magnetic modules?

Scott: Yes, we are using Qiagen magnetic beads for our experiments. One of our goals was to perform phosphopeptide enrichment of iron-NTA. In addition, we also use magnetic beads for peptide desalting. When performing digestion experiments, many times it is necessary to perform it in a buffer containing a high salt content, and then the salt needs to be removed in order to carry out other chemical reactions. When performing ion exchange chromatography, the salts in the buffer also need to be removed first. These are currently tasks that are all done manually, and although we have a vacuum alignment system, the pipetting heads still need to be operated manually. If automation can be achieved, such as using magnetic beads, it will greatly save our workload.

In addition, when we perform matrix-assisted laser desorption ionization (MALDI) analysis, we need to perform desalting treatment and use a ZipTip to operate, and then drop the processed sample on the plate. While this in itself is not difficult, if you need to process a large number of samples, such as 10 samples, repeating this operation for an extended period of time may trigger symptoms of pinched nerves in the hand, also known as carpal tunnel syndrome. If we can use robots to process large sample sets, it will greatly reduce our workload.

Additionally, we are excited about applications in drug discovery. We are currently collaborating with Nathaniel Gray's laboratory to develop and biochemically characterize novel covalent kinase inhibitors. We plan to use the robot to perform kinetic assays by setting up protein reactions with inhibitors and have the robot take the reactants from different time points and drop them onto a MALDI plate, which would be awesome!

As a result, I have a lot of ideas on how to leverage the Opentrons platform to the advantage of multiple projects. I’m sure we’ll have more and deeper ideas as we start experimenting and exploring.

Standardizing mass spectrometry sample preparation through automation

Kristin: Your research using the Opentrons platform focuses on mass spectrometry sample preparation. I understand this saves time and avoids manual fatigue, but other than that, is it of any scientific and technical importance?

Scott: Consistency in sample preparation is critical to obtaining reproducible results. Manual operations alone are time-consuming and difficult to ensure quality. We have many research projects and many collaborations with other laboratories, and time is of the essence. Therefore, flexible automated sample preparation systems allow us to get more done and ensure consistency and reproducibility every experiment. For example, the Opentrons platform can significantly increase the throughput of kinase inhibitor binding assays.

Kristin: So how is it implemented?

Scott: Because the robot can position itself quickly, we can sample the response with good temporal resolution. Moreover, we can do this for multiple compounds simultaneously. This type of information is extremely valuable in many of our projects.

Dagney: Is this why you mainly use MALDI well plates?

Scott: This is just one application. But there are many other applications. For example, we would like to use it for routine intact protein analysis, as well as digest titration to confirm protein ID by MS/MS.

Dagney: As sample preparation improves, you'll get cleaner results and be able to do more with them.

Scott: : Yes, you can spend more time thinking about scientific problems instead of spending it on the lab bench.

Kristin: And share! Our dream is to have you and Stanford do the same thing on the other side of the country and develop these processes.

Scott: Yes, it will make everyone more productive. It will be great to see how everyone develops! I'm very excited about this open source revolution.

The flexibility of open source

Dagney: How many open source devices are there typically in an academic environment?

Scott: As far as I know, there are very few. But that's just because I feel like the open source device trend is just getting started. I've heard that there are a few labs that have 3D printers, and a lot of labs are interested in your robotics platform, but in all the labs I've been in, I really haven't seen any open source equipment. However, with the emergence of exciting open source solutions like yours, I think they will be adopted quickly as they offer many advantages. For example, open source options will help reduce the ever-increasing repair service costs associated with maintaining proprietary instruments.

Kristin: So, how do you think having access to more open source equipment will help you conduct research better?

Scott: A lot of times, as a researcher, you think creatively about how to solve problems. Unfortunately, existing hardwired closed source systems don't allow you to do exactly what you want. In order to complete the task, you may need to change some parts of the software or hardware. These things are very difficult or impossible to achieve with a closed system.

As an example, we have several proprietary robotic platforms in our lab that perform their functions well, but they are not particularly suitable for modification beyond limited operations. Open source platforms like yours will enable rapid prototyping of custom solutions. For example, I don't think you originally thought of the robot as a MALDI spotter; but now that we have developed the OT-1, I believe it is very suitable for spotting samples for MALDI analysis.

Dagney: This is great!

Scott: Yes! So you know, if we want to do something innovative we are fully capable of doing that. With your Python API, I would say... there are really no limits with Opentrons when it comes to customization. As far as I know, this is not possible from a software perspective on any other commercial system. You can't hack these systems, they are all pre-compiled.

Kristin: Yes, most bots basically only provide one way to use them.

Scott: Yes. While commercial vendors try to make their software more flexible, you often run into limitations - and sometimes it's really frustrating because you just need to make some minor software changes - and it only takes someone who knows how to program to spend It takes just a few minutes – and you can enable certain workflows or applications. But getting them to do that is very difficult.

I think they do have good intentions, but they can't see all the use cases, and they don't have enough people to respond to feedback in real time. But having the support you guys provide on Slack is awesome. Did you know? I'll post some questions there and usually get responses and suggestions much faster than expected. It was great working with you guys! I hope everything goes so smoothly!

Dana-Farber Cancer Institute is a global leader in cancer treatment and research. Opentrons remains committed to empowering scientists working on projects of this scale to share their progress with the community.