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Transforming Sample Prep for Mass Spectrometry

3D molecular structure showing protein fragments.
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Mass spectrometry is a key tool for proteomics, but traditional sample preparation methods often limit its potential. Techniques such as laser capture microdissection, antibody-based enrichment and proximity labeling are often constrained by limited resolution, sample type restrictions and the need for prior target knowledge.


These challenges can obscure the discovery of novel protein constituents, particularly in complex biological samples. To fully harness the capabilities of mass spectrometry, new sample prep approaches are needed that offer both precision and flexibility.


At the recent American Society for Mass Spectrometry conference in Baltimore, Technology Networks sat down with Dr. Nikhil Rao, chief commercial officer at Syncell, to learn more about Microscoop®Mint. This advanced sample preparation platform labels and analyzes all proteins within defined regions of interest without pre-selection.


In this interview, Rao delves into the technology behind Microscoop Mint, outlines its key advantages over traditional workflows and discusses how its transforming proteomic profiling across diverse tissue environments.

Bree Foster, PhD (BF):

Could you introduce Microscoop Mint and explain how it differs from traditional sample preparation methods for mass spectrometry? 


Nikhil Rao, PhD (NR):

The Microscoop is aptly named because we’re essentially scooping up proteins from specific subcellular or cellular regions within tissues at extremely high resolution and enables unbiased discovery of new protein constitutents.


Traditionally, researchers have relied on methods like proximity labeling, which involves transfection or other strategies to tag proteins near a region of interest, or laser capture microdissection, which physically cuts out portions of tissue. Both have their limitations.


Our technology is differentiated in the sense that, unlike proximity labeling, it works on virtually any fixed sample – cells, tissue, FFPE, fresh or frozen – and uses imaging to guide precise region selection.


The Microscoop is compatible with human samples, whereas most proximity labeling methods are restricted to mouse and rats. That means we can analyze even decades-old FFPE tissue, for example from brain banks, which significantly expands what’s possible.


Additionally, we provide much higher spatial resolution, down to 350 nanometers in x and y, and about 1.5 microns in z. This is a huge improvement on other techniques, like laser capture microdissection, which gets down to 5–10 microns at the highest resolution. Our z-axis resolution enables precise targeting of specific organelles within a tissue section. This specificity translates to exceptionally high-quality mass spec data with a broad dynamic range and identifies novel proteins that were not known prior. We're routinely detecting thousands of proteins per individual cell.



BF:
Can I ask what inspired the technology? 

NR:

That credit goes to our founder and CEO, Dr. Jung-Chi Liao. Back when he had a lab at Columbia, he was studying primary cilia, tiny structures, just one micron by one micron. He struggled to isolate the proteome of those cilia without extracting proteomic material from other parts of the cell. He even had his postdocs attempting laser cuts to extract them, but nothing worked.


He started developing a solution for himself. He’s been working on this technology for about 11 years now. Eventually, he realized this wasn’t just his problem, there were a lot of researchers facing the same challenge and trying to answer a universally relevant question for researchers in biology, “what are the protein constituents of X organelle in Y cell type.” Around five years ago, he shifted focus from a personal tool to a commercial product, and since then, we’ve grown the company and are now selling the instrument worldwide.



BF:
Could you give us an in-depth explanation of how the technology works?

NR:

Let’s say I’m a researcher interested in mitochondria. My core question might be: what is the proteome of the mitochondria in a control vs. treatment group? Maybe I’m comparing cancerous versus non-cancerous tissue, or treated versus untreated, there are a host of questions that require a hypothesis free view of the proteome.


The researcher can use a single antibody marker to label the mitochondria, just one marker to visualize them so they’re seen under a microscope. That’s the microscopy-guided part of the workflow. Once you can see the mitochondria, we generate an image mask, which is just a simple binary file that flags where those structures are. It’s basically a “yes” for mitochondria and “no” for everything else (we call these regions of interest or ROI’s). That image serves as a blueprint to identify exactly where within your tissue or cell sample you want to target.


Our system aligns that image with the physical sample and then fires a laser at each of those identified ROI’s. At this point, we’ve applied a reagent to the sample that enables a photoactivated biotinylation reaction. This means wherever the laser shines on the tissue or cells, biotin is activated and covalently binds to the proteins in that local area. This process is non-specific; it non-specifically tags protein within the region lit up by the laser.


Once the entire sample is processed, all the mitochondria, and only the mitochondria, have their resident proteins biotinylated. The sample is removed from the instrument and we extract those biotinylated proteins using our own optimized streptavidin bead kit, wash away everything else, and elute the proteins of interest. What you’re left with is just the mitochondrial proteome, ready for mass spectrometry.



BF:
What advantages does Microscoop Mint offer in terms of sample compatibility and unbiased discovery across different tissue types? 

NR:

We can work with a wide range of samples – fresh frozen, PFA-fixed, methanol-fixed, FFPE – you name it. The only thing we do not support is live cells. With antibody-based technologies, you have to ask: do I already know my target of interest? Does this antibody work in FFPE? What about frozen or methanol-fixed tissue? And then, even if it does, does it recognize the protein in human, mouse or rat?


That narrows the scope of discovery pretty quickly. You're funneling your research question into a very specific set of conditions that may or may not work. With Microscoop Mint, we sidestep a lot of that. Because we use biotinylation, which is non-specific, you don’t need that same level of stringency. You still need an antibody or other fluorescent marker for the initial imaging step to define your region of interest, but after that, it’s all handled by light-activated chemistry.


For FFPE samples, for instance, we just deparaffinize, stain with a single antibody, and move forward. The biotinylation reaction itself works across these sample types because it’s light-driven and forms a covalent bond with amino acid residues. That broad compatibility opens the door to more exploratory, unbiased proteomic analysis. 



BF:
In terms of omics, do you think it could be used for metabolomics or lipidomics in the future, or is it quite specific to proteomics?

NR:

Our current on market solution supports only proteomics. But down the line, we could apply this to different omics such as metabolomics, lipidomics and even RNA. There are multiple different directions we could go depending on the researchers needs.



BF:
How has Microscoop Mint been applied in studying complex tissue environments or disease-associated interactions?

NR:

The Microscoop Mint is a Swiss Army knife with respect to applications. If I was to look at the landscape and say who's most interested in this technology, it would be the cell biologists. They're looking at cell-cell interactions, organelle interfaces, membrane proteins, condensates and understanding nuclear protein cell bodies and many more.


But it goes far beyond that. We’ve seen strong adoption in neuroscience, especially from researchers working on neurodegenerative diseases like ALS, Alzheimer’s and Parkinson’s. Those plaques are notoriously hard to isolate, laser capture microdissection struggles with them, and proximity labeling isn’t an option, so our method fills a real gap. Many of our early users have come from the neuro space for that reason.


We’re also seeing growing interest in cancer biology. Researchers are starting to use Microscoop Mint to compare metastatic versus non-metastatic cells and to better understand the tumor microenvironment.


One of the biggest themes at this meeting has been the application of Microscoop Mint for drug discovery, particularly around target identification. Scientists are asking: Can we identify a druggable biomarker in a specific context? Or, if we tag a drug with a fluorescent marker, can we track its movement through the cell and identify the proteins involved in its trafficking? If you can map those proteins, you can potentially redesign the drug to be more effective.