Dina Schuster

All Publications

• A Prototype timsOmni Platform Enables Confident Annotation of the Key Hypervariable CDR3 Regions of IgG Immunoglobulins Using Low- and High-Energy Electron-Based Fragmentation ANALYTICAL CHEMISTRY Ollivier, S., Schuster, D., van Rijswijck, D. M. H., Stroganova, I., Smyrnakis, A., Fiala, J., Kosmopoulou, M., Suckau, D., Pengelley, S., Raether, O., Greisch, J., Papanastasiou, D., Heck, A. J. R. 2026

  Abstract

  The configuration of the first prototype timsOmni instrument, which integrates an Omnitrap linear ion trap into a timsTOF platform, is presented. A modified electrode design for the electron-based fragmentation (ExD) section of the Omnitrap is described, enhancing both the robustness and performance. Optimal characterization of antibodies requires characterizing light and heavy chains as pairs in addition to sequencing their variable domains and identifying any modifications. This is best addressed using protein-centric proteomics, as heterogeneity information such as the specific clonal origin of each identified fragment can be retained. Furthermore, by acting on intact proteins that retain part of their structure, such as disulfide bonds, it is possible to target key regions for fragmentation such as the hypervariable complementarity determining regions (CDR3) that are unique for each clone and necessary for target recognition. Therefore, as a proof of concept, we used the prototype timsOmni mass spectrometer for antibody analysis. Using solely electron-based fragmentation methods, we obtained full CDR3 sequences for paired heavy and light chains. Optimal results were achieved by performing Electron Induced Dissociation (EID) at ∼35 eV electron energy on native-like fragment antigen-binding (Fab) precursor ions. This approach yields both (a, x) and (c, z) fragment ion pairs with the potential to enhance both sequence coverage and annotation confidence. Overall, the timsOmni mass spectrometer presented here serves as an advanced and versatile platform for protein-centric proteomics.

  View details for DOI 10.1021/acs.analchem.5c07288

  View details for Web of Science ID 001734617400001

  View details for PubMedID 41945787

• Mass spectrometry-based strategies for membrane protein pharmacology. Trends in pharmacological sciences Reiter, A. H., Fehr, A., Florea, R., Floyd, B. M., Schuster, D. 2025

  Abstract

  Membrane proteins are essential for cellular physiology and the target of half of all FDA-approved drugs. However, their hydrophobicity and low abundance make large-scale expression and purification difficult, posing a challenge for drug discovery. Despite these problems, mass spectrometry (MS) has enabled workflows for higher-throughput ligand screening, simplified identification of membrane protein targets and ligandable sites, and direct analysis of drug binding in native environments. In this review, we highlight emerging MS-based strategies, adapted workflows, and novel technological advances in different MS-based fields, including affinity selection, probe-based and probe-free chemoproteomics, and native MS that collectively expand our ability to interrogate membrane proteins for drug discovery, target deconvolution, and mechanistic characterization.

  View details for DOI 10.1016/j.tips.2025.10.012

  View details for PubMedID 41271450

• protti: an R package for comprehensive data analysis of peptide- and protein-centric bottom-up proteomics data BIOINFORMATICS ADVANCES Quast, J., Schuster, D., Picotti, P. 2022; 2 (1): vbab041

  Abstract

  We present a flexible, user-friendly R package called protti for comprehensive quality control, analysis and interpretation of quantitative bottom-up proteomics data. protti supports the analysis of protein-centric data such as those associated with protein expression analyses, as well as peptide-centric data such as those resulting from limited proteolysis-coupled mass spectrometry analysis. Due to its flexible design, it supports analysis of label-free, data-dependent, data-independent and targeted proteomics datasets. protti can be run on the output of any search engine and software package commonly used for bottom-up proteomics experiments such as Spectronaut, Skyline, MaxQuant or Proteome Discoverer, adequately exported to table format.protti is implemented as an open-source R package. Release versions are available via CRAN (https://CRAN.R-project.org/package=protti) and work on all major operating systems. The development version is maintained on GitHub (https://github.com/jpquast/protti). Full documentation including examples is provided in the form of vignettes on our package website (jpquast.github.io/protti/).

  View details for DOI 10.1093/bioadv/vbab041

  View details for Web of Science ID 001153137500080

  View details for PubMedID 36699412

  View details for PubMedCentralID PMC9710675