2026
User-defined peptide libraries generated in E.coli enable highly sensitive detection of cancer antigens using DIA on timsTOF instruments and substantially expand the depth of confident immunopeptidomics data for cancer immunotherapy.
Demonstrated that spatial top-down proteomics can identify intact proteoform signatures associated with donor kidney quality, highlighting the potential of proteoforms as biomarkers to improve organ selection for transplantation.
Established multi-level quality control standards through an inter-laboratory benchmark, providing a framework for reproducible and comparable single-cell proteomics across laboratories.
2025
Mapping of tumor-reactive T cells across multiple myeloma and acute myeloid leukemia to uncover conserved immune programs and shared tumor antigens.
Developement of a data independent mass spectrometry workflow for histone post-translational modifications in individual cells to investigate epigentic regulation and overall chromatin heterogeneity at single-cell resolution.
Developed a high-throughput workflow for deep proteomic and phosphoproteomic profiling of archival FFPE tissues.
2024
Book chapter with detailed step-by-step protocol for reproducible label-free single cell proteomics.
Demonstrated an automated label-free single-cell proteomics workflow with sufficient depth and throughput to resolve complex biological processes beyond cell type classification up to 80SPD.
2023
Development of sensitive HLA-I and HLA-II immunopeptidomics workflows on the timsTOF from limited samples to facilitate discovery of tumor-associated antigens and clinically relevant peptides for personalized immunotherapy.
Presentation of the first commercially available solution for single-cell proteomics, the proteoCHIP. Combining multiplexed sample preparation and acquisition for high-throughput, reproducible proteome profiling of thousands of single cells with minimal sample loss.
2021-2022
Demonstrated that self-organizing human cardioids resemble early heart development to study cardiogenesis and congenital heart disease.
Established best practices for multiplexed single-cell proteomics by defining experimental strategies to improve quantitative accuracy while maintaining proteome depth and throughput.
Combined multiplexing with data-independent acquisition to achieve highly reproducible, quantitative proteome profiling across large sample cohorts with minimal missing data.
2019-2020
Developed a chemical proteomics workflow to directly measure off-target effects of the small molecule foretinib in lung cancer cells.
Improved the sensitivity of low-input proteomics by introducing micropillar array chromatography, enabling deeper proteome coverage with reproducible retention times.
Reviewed the emerging field of single-cell proteomics, including technological advances, remaining challenges, and future opportunities.
2017-2018
Developed a comprehensive mass spectrometry workflow to identify malondialdehyde-modified peptides.
Combined chemical and phosphoproteomics with network analysis to uncover the mechanism of action of midostaurin in lung cancer cells, revealing new therapeutic opportunities.
Claudia Ctortecka, Ph.D. 