At core facilities, new technologies don’t just enable experiments — they reshape how researchers think about what questions are even possible to ask. Few people see that transformation as clearly as Tolga Soykan, PhD, an image analyst and microscopy expert at Leibniz Institute for Molecular Pharmacology (FMP) in Berlin.
As part of FMP’s imaging facility, Dr. Soykan supports a broad spectrum of cell biology, neurobiology, and translational research projects. In early 2025, he also took responsibility for operating Syncell’s Microscoop Mint system at FMP — integrating microscopy-guided photolabeling into an already mature imaging and mass spectrometry ecosystem.
What followed wasn’t just a new workflow, but a new way to approach spatial proteomic discovery.
Why FMP Brought Microscoop In-House
Before adopting Microscoop, many of the challenges Tolga and FMP researchers faced were familiar in spatial proteomics.
Biochemical fractionation approaches often struggle with cross-contamination, especially for small, fragile, or closely associated organelles. Proximity labeling methods like BioID, TurboID, or APEX offer access to intact cells, but come with tradeoffs: variable labeling efficiency, background biotinylation, and limited control over what is being labeled.
“Obtaining a specific proteome of a target structure was one of the biggest challenges,” Dr. Soykan explains. “In general, with all of these approaches, we had limited precision in the form of spatial resolution, and we had limited flexibility in deciding exactly what we want to target and isolate.”
Microscoop changed that equation by allowing researchers to visually define the target first, then label it. Instead of inferring spatial proximity biochemically, the region of interest — an organelle, a tissue zone, even a rare cell subtype — is selected directly from images. That shift proved especially valuable for systems where subtle spatial differences matter.
From Synaptosomes to Synapse Subtypes
Dr. Soykan’s background in neurobiology makes synapses a natural example. Traditional synaptosomal fractionation can isolate synapses as a bulk population, but distinguishing different synapse subtypes — which often coexist within the same neuron — has been a long-standing challenge.
“With Microscoop,” he says, “as long as you can visually stain and separate different synapse subtypes, you can understand each of their proteomic profiles.”
That capability opens doors not only for basic neuroscience, but for disease research as well. Many neurodegenerative and neuropsychiatric disorders originate at the synapse, and understanding subtype-specific proteomes could reveal early, previously inaccessible molecular changes.
Establishing the Workflow: Start Simple, Then Expand
At FMP, onboarding the system began with well-defined organelles. The team first targeted nuclei to establish labeling, pulldown, and mass spectrometry workflows. Once confident, they moved on to mitochondria — a more complex test case that required careful image analysis and segmentation strategies.
“We experimented with different segmentation methods,” Dr. Soykan explains, “including selectively targeting peripheral mitochondria and avoiding crowded perinuclear regions.”
Those early experiments helped the team optimize:
- segmentation pipelines
- pixel density required for effective labeling
- number of slides and cells per experiment
- protein concentrations needed for efficient pulldown
Crucially, these optimizations were carried out hand-in-hand with Syncell’s scientific support team, accelerating FMP’s path to reliable, reproducible data.
Ease of Use — for Experts and New Users Alike
Despite Microscoop’s technical sophistication, Dr. Soykan emphasizes its accessibility.
The Nikon epifluorescence microscope provides a robust base microscopy platform with high imaging quality and effective autofocus, which fully integrates with the Microscoop’s automated image scanning to make it a straightforward process for him to start running samples within two to three days.
“I also trained some users who did not have very much microscopy experience, and for them getting started and learning how to set up the automated imaging was quite easy and indeed fun as well,” laughs Tolga.
Importantly, this enables Microscoop to be a shared facility resource, not a niche instrument reserved for specialists.
Beyond Single Cells: A Broad Spatial Spectrum
One of Microscoop’s strengths at FMP has been its flexibility across scales.
“Single cell proteomics is on the rise,” observes Soykan, “It’s advancing very rapidly. But it also often requires very specialized and complex methods that may not be accessible to every lab. What Microscoop provides is a more accessible and more cost-effective alternative that integrates into existing workflows.”
This means that researchers can move fluidly from:
- tissue regions
- to specific single cell populations
- down to nanoscopic structures within cells
“Beyond profiling distinct cell types,” Soykan notes, “it allows us to proteomically fingerprint specific organelles or any structure that can be visually defined. That level of spatial specificity simply isn’t achievable with non-visual approaches.”
Complementary, Not Competitive, with Existing Spatial Tools
Dr. Soykan positions Microscoop as complementary to established spatial and super-resolution imaging methods.
Techniques like STED or STORM excel at measuring precise molecular distances — for example, mapping vesicle positions relative to synaptic active zones. But they are less suited for unbiased discovery of novel proteome components.
Microscoop bridges that gap by pairing spatial specificity with mass spectrometry–based readouts, offering discovery-driven insight that can later inform targeted imaging or functional follow-up.
White-Glove Support — and Why It Matters
A recurring theme in Dr. Soykan’s experience is the importance of close scientific collaboration during setup.
At FMP, Syncell provided:
- in-person installation and training
- hands-on support for early experiments and mass spec submission
- test samples and reference datasets for alignment
- advanced help with mask generation and segmentation edge cases
That support enabled FMP to feel confident in their data early — and to quickly transition Microscoop from a pilot system into a service offering.
An Expert’s Recommendation for New Projects
Today, Dr. Soykan actively advises researchers on which projects are well-suited for Microscoop and supports both internal users and external collaborations through FMP.
“If you can visualize your structure of interest,” he says, “then Microscoop is worth considering.”
For groups seeking spatially resolved proteomics — particularly where traditional fractionation or proximity labeling falls short — FMP now offers end-to-end Microscoop expertise, from experimental design through mass spectrometry analysis.
Looking Forward
Reflecting on the technology, Dr. Soykan returns to a sentiment familiar to many scientists encountering a genuinely new tool:
“The more new techniques you learn, the more you reflect about the past — what you could do, or what you can still do.”
With Microscoop now established at FMP, those reflections are increasingly turning into new experiments (and new data!) that simply were not possible before.
