3rd International Top-Down Proteomics Symposium

Session

New approaches for proteoform analysis

Aug 28, 2025, 10:20 AM

VMP 6 / Philturm (Lecture Hall D)

49. Advances in Orbitrap mass spectrometry for top-down analysis

Alexander Makarov (Thermo Fisher Scientific (Bremen) GmbH)

8/28/25, 10:20 AM

Oral Presentation

The analysis of intact proteins and protein complexes presents unique challenges to mass spectrometry (MS), prompting a fundamental re-evaluation of principles previously validated for small molecules and peptides. As the initial limitations of fragmentation have largely been overcome in the past two decades—culminating in near-complete freedom of fragmentation in the latest instruments—severe...

91. Exploring Spatial Top-Down Proteomics

Ljiljana Paša-Tolić (Pacific Northwest National Laboratory, Richland, WA 99354, USA)

8/28/25, 10:40 AM

Oral Presentation

Understanding proteins within their functional contexts, whether in tissue units, cellular neighborhoods, small clusters of cells, or even at the single-cell level, remains a significant scientific challenge that pushes the boundaries of analytical methods. Traditional proteomic approaches largely rely on antibody-based techniques, which limit multiplexing and require prior knowledge of target...

14. Exploring the effects of isotope depletion on proteins by native mass spectrometry and cryogenic electron microscopy

Anjusha Mathew

8/28/25, 11:00 AM

Oral Presentation

Isotope depleted protein samples have successfully addressed various challenges in native mass spectrometry (MS), notably by enhancing the signal-to-noise (S/N) ratio- an advantage particularly beneficial for high molecular weight protein analysis. In this study, we explore the broader impact of isotope depletion on reducing sample heterogeneity, and enhancing mass spectral quality in MS, as...

60. Discovering the ‘negative’ side of the proteomic landscape with top-down mass spectrometry

Cynthia Nagy (University of Oklahoma)

8/28/25, 11:15 AM

Oral Presentation

Conventional mass spectrometry-based proteomics use positive polarity and provide a wealth of qualitative and quantitative information; however, these methods may not capture the true complexity of the proteome. Our work aims at alleviating this issue by resorting to ionization in negative polarity to account for the acidic portion of the intact proteome that preferentially ionizes as anions....

31. Glycoproteomics Based on Deep Learning and Data Independent Acquisition

Liang Qiao (Fudan University)

8/28/25, 11:30 AM

Oral Presentation

Large-scale profiling of intact glycopeptides is critical but challenging in glycoproteomics. In 2021, we propose GproDIA [1], a framework for the proteome-wide characterization of intact glycopeptides from DIA data with comprehensive statistical control by a 2-dimentional false discovery rate approach and a glycoform inference algorithm, enabling accurate identification of intact...

46. High resolving power meets proton transfer charge reduction: unlocking new depths in intact protein characterization

Rafael D. Melani (Thermo Fisher Scientific, San Jose)

8/28/25, 11:45 AM

Oral Presentation

Although the characterization of intact proteins remains a demanding endeavour – particularly as protein size increases - ongoing technological/bioinformatic advancements are steadily enhancing the capabilities of top-down mass spectrometry (TDMS) for deep sequencing. Different ion activation techniques – such as electron transfer dissociation (ETD), electron transfer higher-energy collisional...