3rd International Top-Down Proteomics Symposium

Session

Poster Session 2

Aug 28, 2025, 1:00 PM

VMP 6 / Philturm (Lecture Hall D)

72. Applying cDDA-ExD on a timsOmni to the analysis of the Fab regions of antibodies originating from human serum

Jean-Francois Greisch (Bruker Switzerland AG)

Poster

Introduction
Protein-centric proteomics is an emerging mass spectrometric field where to answer a biological question related to cells or tissues, one analyzes proteins directly, without relying on their digestion into smaller peptides. The unique ability of protein-centric proteomics to disentangle isoforms and proteoforms is directly beneficial to the complex functional analysis usually...

74. Assessment of the small protein proteomes of Methanosarcina mazei under different stress conditions using a combination of top-down and bottom-up proteomics.

Liam Cassidy (Kiel University)

Poster

Short open reading frame (sORF) encoded proteins fulfil important roles in many cellular processes. In the methanoarchaeon Methanosarcina mazei, numerous small proteins have previously been identified under different nitrogen availabilities, however, few have been functionally characterised. Consequently, a detailed analysis of small proteins translated under a range of growth conditions may...

68. Detection of intact bovine milk protein after gastrointestinal digestion using UHPLC-HRMS

Hannah Zenker

Poster

The presence and relative abundance of intact protein after gastrointestinal digestion is an important aspect of the evaluation of digestion efficiency and the assessment of protein allergenicity. The detection of intact proteins after gastrointestinal digestion is commonly done using gel electrophoretic applications (SDS-PAGE). These are highly sensitive, however in some cases SDS-PAGE does...

76. ETD / EThcD functionality on the novel Orbitrap Excedion Pro mass spectrometer

Cong Wang

Poster

Electron-transfer dissociation (ETD) is a well-established technique, where fragmentation is caused in cationic precursors by electron transfer from a donor molecule. While ETD/EThcD is already present in the family of Orbitrap Tribrid mass spectrometers, using Fluoranthene as an electron donor, this functionality is missing on the Orbitrap Hybrid mass spectrometers. With the Orbitrap Excedion...

26. Identification and quantification of methionine oxidation in monoclonal antibody using middle-down proteomics with electron activated dissociation

Abdulafeez Akinloye (University of South Australia, Adelaide, Australia)

Poster

Methionine oxidation is one of the most frequently observed post-translational modifications of monoclonal antibody (mAb) products during their development and production that can affect the drug’s safety and efficacy. Such modifications are typically assessed using bottom-up peptide mapping techniques. However, this methodology is often tedious and prone to the generation of artefacts through...

66. Illuminating Proteins: Dual UV/IR Photodissociation in a custom FT-ICR system

Ms Ezgi Gürler (BIOCEV - Institute of Microbiology, Czech Academy of Sciences; Faculty of Science, Charles University in Prague)

Poster

Top-down mass spectrometry (TDMS) elucidates the molecular weight, characterizes proteoforms, and, in its native form, can even inform binding stoichiometry and higher-order structure of proteins and their complexes. The information gained is, however, largely dependent on the protein system in question and the dissociation technique used. Therefore, there is a great need for more efficient...

70. Mapping transient, short linear motif-mediated protein-protein interactions using photo-crosslinking top-down mass spectrometry

Yee-Man Michelle Pang (EaStCHEM, School of Chemistry, University of Edinburgh)

Poster

Protein–protein interactions (PPIs) govern countless biological processes and range from stable, permanent complexes to transient, short-lived ones. Among the latter, short linear motifs (SLiMs) play a critical role by mediating low-affinity, transient interactions. These are essential for cellular functions like directing protein localization through targeting signals. However, due to their...

84. MS-based characterization of clinically relevant glycoproteoforms

Yuri van der Burgt (Leiden University Medical Center)

Poster

Dynamically altering biomolecules are the true actors in studies on health and disease rather than genotypes or phenotypes that refer to a certain risk or an end-point observation. Unfortunately, clinically effective disease-specific tests that support diagnoses at an early and curable stage are still lacking for a wide variety of diseases. Proteoform-resolved data provides a layer of...

40. Multi-scale mass analysis for the characterization of engineered DNA assemblies

Elisabetta Boeri Erba (Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France)

Poster

Nucleic acids (DNA, RNA, artificial analogues such as TNA) can form remarkable three-dimensional structures, which play key roles in biology and nanobiotechnology. In the field of DNA nanotechnology, static or dynamic nucleic acid assemblies have applications in biotechnology, nanomedicine, nanophotonics and nanoelectronics. Determining the size, shape and assembly route of oligomeric nucleic...

86. nQuant Enables Precise Quantitative N-Glycomics

Shanshan Zhao (University Hamburg)

Poster

Abstract: N-glycosylation, as the most complex post-translational modification of proteins, involves crucial biological functions. It has been demonstrated that aberrant N-glycosylation is directly linked to various human diseases, while mass spectrometry-based N-glycomics still lags behind, limiting the in-depth mining of glycobiological information. Aiming to rectify the bias of the previous...

82. Probing Human Oocyte Heterogeneity by Single Cell Proteoform Imaging Mass Spectrometry

Nickolas Fisher (Department of Chemistry and Molecular Biosciences, Northwestern University, Evanston, IL, USA.)

Oral Presentation

Ovarian tissue cryopreservation (OTC) is utilized by clinics to preserve oocytes and immature eggs for pediatric patients who are at increased risk of becoming infertile due to a diagnosis or treatment. Late-stage oocytes, that are not yet mature, are often released during OTC. We are interested in identifying proteoforms that may improve in vitro maturation of oocytes into eggs for these...

80. Quantification of monoclonal antibodies by middle-up capillary electrophoresis-mass spectrometry

Jana Havlikova (Comenius University Bratislava)

Poster

Monoclonal antibodies (mAbs) are biopharmaceuticals widely used in treatment of various diseases. Due to their intrinsic complexity and post-translational modifications, therapeutic mAbs are highly heterogeneous molecules requiring extensive quality control. Quantitative analysis typically relies on liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) and the gold-standard...

62. Selective comprehensive online nanoLCxCZE-MS platform for top-down proteoform analysis

Tobias Waldmann (Aalen University)

Poster

Capillary zone electrophoresis-mass spectrometry (CZE-MS) has been used to separate proteoforms on intact protein levels, however, sensitivity and selectivity are often not sufficient for complex biological samples. We therefore developed a two-dimensional (2D) heart-cut nanoLC-CZE-MS platform and showed that this allows the pre-separation of intact proteins from a complex matrix and a...

64. Top-Down Mass Spectrometry in a Service Environment: Insights from User Projects and Workflow Implementation

Natalia Gasilova (EPFL)

Poster

Top-down mass spectrometry (TD MS) is a powerful approach for the in-depth analysis of protein modifications, offering detailed, and sometimes unique, insights into intact proteoform structures. As the demand for proteoform-level information grows in biomarker discovery, drug development, and structural biology, there is increasing need for specialized fee-for-service (core) facilities...