Claudia Ctortecka, Ph.D.
Mass spectrometrist at heart.
About me.
I am a proteomics researcher and independent unit lead at Amsterdam UMC and VU Amsterdam, where I lead the SCAPE unit at the intersection of cancer biology and neurodevelopment. Originally from Vienna, I am building a research program around single-cell and spatial proteomics developing the tools, workflows, and conceptual frameworks needed to decode cellular identity and disease heterogeneity imprinted in the proteome.
My lab focuses on mass spectrometry-based proteomics applied to characterize complex tissues with particular focus of neurodegeneration. We believe that protein-resolved measurements are essential for understanding how cell states are encoded and dysregulated in disease. For this, we develop integrated experimental and computational approaches that connect single-cell resolution or spatial context with molecular precision.
I am also the chair of the Single Cell Initiative at the Human Proteome Organization, where I work to establish community standards for reproducible, transparent, and cross-laboratory single-cell proteomics research.
Scientific Journey
My path to single-cell and spatial proteomics has been shaped by a series of fantastic mentors, each one shaping how I approach science and provide novel solution to answer challenging new biological questions.
It started with the very small, during a research stay at Stockholm University, I studied the broad impact of a single protein essential for airway development in Drosophila melanogaster. At the Moffitt Cancer Center with Uwe Rix, I moved from model organisms into human disease. Combining chemical proteomics with global and phosphoproteomics, we identified unexpected activity of an FDA-approved leukemia therapeutic in non-small cell lung cancer, a direct demonstration of what proteomics-driven drug repurposing could look like in practice.
My doctoral work with Karl Mechtler and Sasha Mendjan at the Vienna Biocenter pushed that further, into the challenge of working with individual mammalian cells. In close collaboration with Cellenion we developed the first commercially available single-cell proteomics workflow using automated isobaric labeling and sample pooling with direct connection to liquid chromatography. As a postdoctoral researcher in Steve Carr’s group at the Broad Institute of MIT and Harvard, I pushed that sensitivity to its limits, advancing single-cell and spatial proteomics workflows for direct single-cell measurements. Most recently, as a CLP Translational Proteomics Fellow at Northwestern University with Neil Kelleher, I developed high-throughput arrays for single-cell top-down proteomics, moving from peptide-level snapshots to intact proteoform measurements at population scale. In combination, that work is the direct foundation of what my group is now pursuing in Amsterdam.
In brief.
From organ development in fruit flies, to drug target identification in lung cancer, to pushing mass spectrometry sensitivity to the level of individual cells, to resolving intact proteoforms within spatial tissue architecture. I aim to understand how molecular complexity maps onto biological function, one cell at a time.
When I’m not at the mass spectrometer, you’ll find me running and, in true Austrian tradition, seeking out a good brewery after a long hike.
Claudia Ctortecka, Ph.D. 