Publications

2026

Kasidet Manakongtreecheep*, Claudia Ctortecka*, Luis O. Correa-Medero, Timothy Zhu, Isabelle Lippincott, Griffin M. Lawrence, Alexis Howard, Gabrielle M. Hernandez, Cleo Forman, Emma C. Duggan, Marta A. Wilbrink, Eva K. Verzani, Alexander B. Afeyan, Jiaxun Li, Alexey I. Nesvizhskii, Giacomo Oliveira, Derin B. Keskin, Patrick A. Ott, Karl R. Clauser, Matthew Bakalar, Siranush Sarkizova, Nir Hacohen#, Steven A. Carr#, Jennifer G. Abelin# & Catherine J. Wu#. “Sensitive detection of cancer antigens enabled by user-defined peptide libraries”. (* authors contributed equally; # shared correspondence)
Nature Biotechnology, February, 2026.
https://doi.org/10.1038/s41587-026-03003-9
Claudia Ctortecka*, Dinesh Jaishankar*, 
Pei Su, Che-Fan Huang, Indira Pla, Nathaniel Henning,  Michael A. R. Hollas, Michelle A. Callegari, Meredith E. Taylor, Yu Min Lee, Amna Daud, David F. Pinelli, Vinayak Rohan, Michael A. Caldwell, Eleonora Forte, Aniel Sanchez, 
Neil L. Kelleher#, Satish N. Nadig#. “Top-Down Proteomics in the Assessment of Kidney Donor Quality: a novel approach to increased organ utilization”. (* authors contributed equally; # shared correspondence)
medRxiv, February, 2026.
https://doi.org/10.64898/2026.02.02.26345404

2025

Tim R. Wagner, Niklas Kehl, Simon Steiger, Tamara Boschert, Michael Kilian, Kane Foster, Gabrielle M. Hernandez, Claudia Ctortecka, Julius Michel, Antonia Schach, Julian Zoller, Anna Metzler, René Onken, Bruno Schönfelder, Simon Renders, Claudia Maldonado Torres, Lilli S. Sester, Jan H. Frenking, Franziska Werner, Wolfram Osen, Katharina Lindner, Ezgi Sen, Sabrina Schumacher, Daria Galas-Filipowicz, Evie Fitzsimons, Edward W. Green, Patrick Schmidt, John M. Lindner, Sebastian Uhrig, Lukas Bunse, Benny Chain, Hartmut Goldschmidt, Niels Weinhold, Stefan Fröhling, Andreas Trumpp, Jennifer G. Abelin, Steven A. Carr, Kwee Yong, Carsten Müller-Tidow, Karsten Rippe, Marc S. Raab, Michael Platten, Stefan B. Eichmüller, Mirco J. Friedrich. “Conserved programs and specificities of T cells targeting hematological malignancies”
bioRxiv, August, 2025.
https://doi.org/10.1101/2025.08.07.668919
Ronald Cutler*, Laura Corveleyn*, Claudia Ctortecka*, Francesca LiCausi, Joshua Cantlon, Alvaro Sebastian Vaca Jacome, Dieter Deforce, Jan Vijg, Maarten Dhaenens, Malvina Papanastasiou#, Steven A Carr#, Simone Sidoli#. “Mass Spectrometry-based Profiling of Single-cell Histone Post-translational Modifications to Dissect Chromatin Heterogeneity”. (* authors contributed equally; # shared correspondence)
Nature Communications, December, 2025.
https://doi.org/10.1038/s41467-025-66031-0
Moe Haines, John R. Thorup, Simone Gohsman, Claudia Ctortecka, Chelsea Newton, Dan C. Rohrer, Galen Hostetter, D.R. Mani, Michael A. Gillette, Shankha Satpathy, Steven A. Carr. “High-Throughput Proteomic and Phosphoproteomic Analysis of Formalin-Fixed Paraffin-Embedded Tissues”
Molecular and Cellular Proteomics, September, 2025.
https://doi.org/10.1038/s41467-024-49651-w

2024

David Hartlmayr, Claudia Ctortecka, Rupert Mayer, Karl Mechtler & Anjali Seth. “Label-Free Sample Preparation for Single Cell Proteomics” Mass Spectrometry Based Single Cell Proteomics, 1-7, June, 2024.
https://doi.org/10.1007/978-1-0716-3934-4_1
Claudia Ctortecka#, Natalie M Clark, Brian W Boyle, Anjali Seth, DR Mani, Namrata D Udeshi, Steven A Carr#. “Automated single-cell proteomics providing sufficient proteome depth to study complex biology beyond cell type classifications”. (# shared correspondence) Nature Communications 15, July, 2024.
https://doi.org/10.1038/s41467-024-49651-w

2023

Kshiti Meera Phulphagar*, Claudia Ctortecka*, Alvaro Sebastian Vaca Jacome, Susan Klaeger, Eva K. Verzani, Gabrielle M. Hernandez, Namrata D. Udeshi, Karl R. Clauser, Jennifer G. Abelin, Steven A. Carr. “Sensitive, High-Throughput HLA-I and HLA-II Immunopeptidomics Using Parallel Accumulation-Serial Fragmentation Mass Spectrometry”.
(* authors contributed equally) Molecular & Cellular Proteomics 22, June, 2023. https://doi.org/10.1016/j.mcpro.2023.100563.
Claudia Ctortecka*, David Hartlmayr*, Anjali Seth, Guilhelm Tourniaire, Namrata D. Udeshi, Steven A. Carr# and Karl Mechtler#. “An Automated Nanowell-Array Workflow for Quantitative Multiplexed Single-Cell Proteomics Sample Preparation at High Sensitivity”. (* authors contributed equally; # shared correspondence) Molecular & Cellular Proteomics 22, December, 2023.
https://doi.org/10.1016/j.mcpro.2023.100665

2022

Claudia Ctortecka, Gabriela Krššáková, Karel Stejskal, Josef M. Penninger, Sasha Mendjan, Karl Mechtler, and Johannes Stadlmann. “Comparative Proteome Signatures of Trace Samples by Multiplexed Data-Independent Acquisition.” Molecular & Cellular Proteomics 21, January, 2022). https://doi.org/10.1016/j.mcpro.2021.100177.

2021

Claudia Ctortecka, Karel Stejskal, Gabriela Krššáková, Sasha Mendjan, and Karl Mechtler. “Quantitative Accuracy and Precision in Multiplexed Single-Cell Proteomics.” Analytical Chemistry, December, 2021,

https://doi.org/10.1021/acs.analchem.1c04174.

Pablo Hofbauer*, Stefan M. Jahnel*, Nora Papai*, Magdalena Giesshammer, Alison Deyett, Clara Schmidt, Mirjam Penc, Katherina Tavernini, Nastasja Grdseloff, Christy Meledeth, Lavinia Ginistrelli, Claudia Ctortecka, Sejla Salic, Maria Novatchkova and Sasha Mendjan. “Cardioids Reveal Self-Organizing Principles of Human Cardiogenesis.”. (* authors contributed equally) Cell, May 20, 2021. https://doi.org/10.1016/j.cell.2021.04.034.

2020

Claudia Ctortecka and Karl Mechtler. “The Rise of Single-Cell Proteomics.” Analytical Science Advances, December, 2020. https://doi.org/10.1002/ansa.202000152.

2019

Johannes Stadlmann, Otto Hudecz, Gabriela Krššáková, Claudia Ctortecka, Geert Van Raemdonck, Jeff Op De Beeck, Gert Desmet, Josef M. Penninger, Paul Jacobs, and Karl Mechtler. “Improved Sensitivity in Low-Input Proteomics Using Micro-Pillar Array-Based Chromatography.” Analytical Chemistry, October 15, 2019. https://doi.org/10.1021/acs.analchem.9b02899.

Natalia J. Sumi, Claudia Ctortecka, Qianqian Hu, Annamarie T. Bryant, Bin Fang, Lily L. Remsing Rix, Muhammad Ayaz, “Divergent Polypharmacology-Driven Cellular Activity of Structurally Similar Multi-Kinase Inhibitors through Cumulative Effects on Individual Targets.” Cell Chemical Biology 26, no. 9 (September 19, 2019): 1240-1252.e11. https://doi.org/10.1016/j.chembiol.2019.06.003.

2018

Claudia Ctortecka, Vinayak Palve, Brent M. Kuenzi, Bin Fang, Natalia J. Sumi, Victoria Izumi, Silvia Novakova, Fumi Kinose, Lily L. Remsing Rix, Eric B. Haura, Matthew Koomen, Uwe Rix. “Functional Proteomics and Deep Network Interrogation Reveal a Complex Mechanism of Action of Midostaurin in Lung Cancer Cells.” Molecular & Cellular Proteomics 17, no. 12 (December 1, 2018): 2434–47. https://doi.org/10.1074/mcp.RA118.000713.

2017

Juliane Weißer, Claudia Ctortecka, Clara J. Busch, Shane R. Austin, Karin Nowikovsky, Koji Uchida, Christoph J. Binder, and Keiryn L. Bennett. “A Comprehensive Analytical Strategy To Identify Malondialdehyde-Modified Proteins and Peptides.” Analytical Chemistry 89, no. 7 (April 4, 2017): 3847–52. https://doi.org/10.1021/acs.analchem.6b05065.