
Claudia Ctortecka, Ph.D.
Mass Spectrometrist at heart.
About me.
I develop technologies that enable protein measurements in individual cells and tissues, revealing biology that is masked by conventional bulk proteomics. Within my single-cell and spatial proteomics unit at Amsterdam UMC and VU Amsterdam we intersect cancer biology and neurodevelopment.
We believe that protein-resolved measurements are essential for understanding how cell states are encoded and dysregulated in disease. Using our tools, workflows, and conceptual frameworks we aim to decode cellular identity and disease heterogeneity imprinted in the proteome of each cell.
I currently serve as the chair of the Single Cell Initiative at the Human Proteome Organization, where we 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.

My first exposure to mass spectrometry in the group of Keiryn Bennett where I supported the team with regular upkeeping of the instruments and the characterization of crosslinked synthetic peptides.
I studied the broad impact of a single protein essential for airway development in Drosophila melanogaster. During my internship with Christos Samakovlis at Stockholm University we investigated the formation of functional airways.
Under the mentorship of 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. In close collaboration with the immunopeptidomics group led by Jenn Abelin we developed E.coli-based peptide expression systems to generate spectral libraries at high-throughput.
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 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.