The paper integrates single-cell proteomics and transcriptomics to study human hematopoietic stem and progenitor cells, identifying protein markers and dynamics not captured by mRNA alone.

Science · Aug 21, 2025Peer-reviewedCell Biology

Quantitative Label-Free Single-Cell Proteomics on the Orbitrap Astral MS

Valdemaras Petrosius, Pedro Aragon-Fernandez, Tabiwang N. Arrey, Jakob Woessmann, Nil Üresin, Bauke de Boer, Jinyu Su, Benjamin Furtwängler, Hamish I. Stewart, Eduard V. Denisov, Johannes Petzoldt, Amelia C. Peterson, Christian Hock, Eugen Damoc, Alexander Makarov, , Erwin M. Schoof

This study evaluates the Orbitrap Astral MS's sensitivity for single-cell proteomics, showing improved proteome coverage and quantitative accuracy in low-input samples.

Molecular & Cellular Proteomics · May 5, 2025Peer-reviewedBiochemistry

Unraveling the proteome landscape of mouse hematopoietic stem and progenitor compartment with high sensitivity low-input proteomics

Nil Üresin, Valdemaras Petrosius, Pedro Aragon-Fernandez, Benjamin Furtwängler, Erwin M. Schoof, Bo Torben Porse

This study develops a low-input proteomics workflow to analyze rare hematopoietic stem and progenitor cells, identifying 7,000 proteins and a novel marker for long-term hematopoietic stem cells.

bioRxiv · May 3, 2024 · PreprintCell Biology

Assessing the role of trypsin in quantitative plasma- and single-cell proteomics towards clinical application

Jakob Woessmann, Valdemaras Petrosius, Nil Üresin, David Kotol, Pedro Aragon-Fernandez, Andreas Hober, Ulrich auf dem Keller, Fredrik Edfors, Erwin M. Schoof

The paper evaluates the impact of different trypsin variants on proteomics experiments across multiple sample types and methods, identifying variations in performance and providing handling recommendations.

Analytical Chemistry · Aug 28, 2023Peer-reviewedMolecular Biology

Evaluating the capabilities of the Astral mass analyzer for single-cell proteomics

Valdemaras Petrosius, Pedro Aragon-Fernandez, Tabiwang N. Arrey, Nil Üresin, Benjamin Furtwängler, Hamish Stewart, Eduard V. Denisov, J. Petzoldt, Amelia C. Peterson, Christian Hock, Eugen Damoc, Alexander Makarov, Vlad Zabrouskov, Bo Torben Porse, Erwin M. Schoof

This study evaluates the Astral mass analyzer's performance in single-cell proteomics using DIA, showing improved proteome depth and quantitative precision for ultra-low input samples.

bioRxiv · Jun 6, 2023 · PreprintSystems Biology

Enhancing single-cell proteomics through tailored Data-Independent Acquisition and micropillar array-based chromatography

Valdemaras Petrosius, Pedro Aragon-Fernandez, Nil Üresin, Teeradon Phlairaharn, Benjamin Furtwängler, Jeff Op De Beeck, Simon Francis Thomsen, Ulrich auf dem Keller, Bo Torben Porse, Erwin M. Schoof

The paper develops a tailored DIA method for single-cell proteomics to improve quantification from low-input samples and establishes a complete scp-MS workflow.

bioRxiv · Nov 29, 2022 · PreprintSystems Biology

Chromosome Compartments on the Inactive X Guide TAD Formation Independently of Transcription during X-Reactivation

Moritz Bauer, Enrique Vidal, Eduard Valera Zorita, Nil Üresin, Stefan F. Pinter, Guillaume J. P. Filion, Bernhard Payer

The paper shows that TAD formation on the inactive X occurs before transcription during X-reactivation, independent of transcriptional activity.

Nature Communications · Jun 9, 2021Peer-reviewedGenomics

Quantitative Single-Cell Proteomics as a Tool to Characterize Cellular Hierarchies

Erwin M. Schoof, Benjamin Furtwängler, Nil Üresin, Nicolas Rapin, Simonas Savickas, Coline Gentil, Eric R. Lechman, Ulrich auf dem Keller, John Edgar Dick, Bo Torben Porse

The paper presents a workflow for single-cell proteomics to study cellular heterogeneity in leukemia, demonstrating the ability to quantify thousands of proteins per cell.

Nature Communications · Jun 7, 2021Peer-reviewedSystems Biology