3rd International Top-Down Proteomics Symposium (ITDP 2025)

The symposium will focus on top-down proteomics, the analysis of intact proteins and protein complexes using high-resolution mass spectrometry. Top-down proteomics is an emerging technology that offers an unprecedented level of accuracy in the detection of differentially modified intact proteins (proteoforms) or associated complexes.

Over the last decade, significant progress has been made in advancing top-down proteomics (both in denatured and native conditions). As a result, interest in top-down proteomics has grown considerably and a number of studies have already demonstrated the potential of this ground-breaking technique for elucidating disease mechanisms and discovering new biomarkers.

In this program, the world's leading experts in top-down proteomics will present the most advanced technologies and approaches.

Registration

Register for ITDP 2025

Registration fees

Early-Bird (to 7. 7. 2025)

• Regular: €400
• Students**: €200

General

• Regular: €500
• Students**: €250

Short Courses (Course 1 / Course 2)

• Regular: €250 /€100
• Students**: €75 / €30

**Proof of student status required during registration.

Abstract Submission

Please submit your abstract here!

Deadlines:

• Oral Presentation:  Now until 07.07.2025 11:59 CET!
• Poster: 15.07.2025

In Indico, you will able to track your submissions.

During the conference, you can view the timetable and find the book of abstracts!

For question regarding the abtract submssion, please fill out the contact form.

Program

The symposium will highlight cutting-edge developments in top-down proteomics, from sample preparation and separation technologies to native MS, bioinformatics, and the analysis of proteoforms and PTMs. Applications in biomedical research, therapeutic proteins, and proteoform function will also be featured!

Tue, August 26

3:15 – 3:30 PM Welcome Session

3:30 – 3:55 PM New Frontiers in Proteomics – Proteoforms, Proteoform Families, and the Human Proteoform Project

• Lloyd Smith (University of Wisconsin–Madison)

3:55 – 4:20 PM Digitizing Proteoform Biology with Single Molecule & Single Cell Mass Spectrometry

• Neil Kelleher (Northwestern University)

4:20 – 4:45 PM Revealing Functional Proteoforms by Native Top-Down Proteomics

• Joseph Loo (University of California, Los Angeles)

4:45 – 5:10 PM Touching upon the Millions of Hidden Treasures in the Plasma Proteome

• Albert Heck (Utrecht University)

5:10 – 6:10 PM Round Table Discussion: Why do we need proteoform-centric research in life sciences?

• Panel discussion

6:15 – 9:00 PM Welcome Reception

Wed, August 27

8:30 – 8:50 AM Advances in Hardware Design and Function of the New timsOmni MS Platform

• Dimitris Papanastasiou (Bruker Daltonics)

8:50 – 9:10 AM Top-down Sequencing of Intact, Modified Proteins by timsTOF Technology with New Multi-modal Fragmentation Capabilities

• Ole Nørregaard Jensen (University of Southern Denmark)

9:10 – 9:30 AM Sensitive Top-down Analysis using Spray-capillary-based CE-MS Approaches

• Si Wu (University of Oklahoma)

9:30 – 9:45 AM Combining Advanced Fragmentation Techniques and Spectral Simplification for Deep Proteoform Interrogation

• Luca Fornelli (University of Oklahoma)

9:45 – 10:00 AM Mass-Invariant Log-Transformed Mass Spectra Enable De Novo Sequencing and Internal Calibration of Intact Proteins

• Lissa C. Anderson (Thermo Fisher Scientific)

10:00 – 10:30 AM Coffee Break

10:35 – 10:40 AM Properties, Origin, and Reproducibility of Truncated Proteoforms Across Top-Down Proteomic Studies

• Philipp T. Kaulich (Goethe University Frankfurt)

10:40 – 10:45 AM Novel Bridged Hybrid Monolithic Columns Combined with Mass Spectrometry for Top-down Proteomic Analysis

• Yu Liang (Dalian Institute of Chemical Physics)

10:45 – 10:50 AM Spatial Phosphoproteomic Profiling of Murine Heart via TiO₂ Enrichment for Laser-Capture Microdissected Samples

• Dan Zhao (University of Wisconsin–Madison)

10:50 – 10:55 AM FLASHApp: Interactive Data Analysis and Visualization for Top-Down Proteomics

• Tom David Müller (University of Freiburg)

10:55 – 11:00 AM Metabolomics and Proteomics Reveal the Inhibitory Effect of Lactobacillus crispatus on Cervical Cancer

• Lingyan Zhong (Xiamen University)

11:00 – 11:05 AM SEC-complex-down Approaches with Functional O₂-affinity Assay: Structure–Function Correlation in Bird Hemoglobins

• Léa Letissier (CNRS)

11:05 – 11:10 AM Multi-dimensional High-Throughput Molecular Glue Screening via Native MS and Cryo-EM

• Amanda Lee (University of British Columbia)

11:10 – 11:15 AM Legionella Effector AnkX Puts the Brakes on IMPDH2 Filaments

• Marietta Sandkamp-Kaspers (University of Münster)

11:15 – 11:20 AM Building a Gold Standard Top-Down MS Dataset for Expanding Simulation Models Across Platforms

• Marie Yammine (ETH Zürich)

11:20 – 11:25 AM X-ray Spectroscopy Meets Native Mass Spectrometry: Probing Gas-phase Protein Complexes

• Jocky Chun Kui Kung (Chinese University of Hong Kong)

11:25 – 11:30 AM A Prototype TIMS-FT-ICR MS Instrument for Deep Characterisation of Complex Samples

• Christopher Wootton (Bruker Daltonics)

11:30 – 11:35 AM Pinpointing Phosphorylation-dependent Pin1 Binding in Alzheimer’s Disease Using Structural MS

• Nikolas Brooks (University of York)

11:35 – 11:40 AM Enhancing Drug-Payload Localization in ADCs via Middle-down Approach with PTCR on Orbitrap Ascend

• Rachel Grady (Thermo Fisher Scientific)

11:40 – 11:45 AM TBA

12:00 – 1:00 PM Lunch Break

1:00 – 1:45 PM Poster Session 1

1:45 – 2:05 PM Uncovering the Unique Properties of Circulating Proteasomes: A Mass Spectrometry Perspective

• Michal Sharon (Weizmann Institute of Science)

2:05 – 2:25 PM Flying Viruses – Mass Spectrometry Meets X-rays

• Charlotte Uetrecht (CSSB Hamburg)

2:25 – 2:40 PM Filling the Structural Knowledge Gap in Protein Design via Native Mass Spectrometry

• Mowei Zhou (Pacific Northwest National Laboratory)

2:40 – 3:10 PM Coffee Break

3:10 – 3:30 PM Replacing “OR” Logic with “AND/OR” Logic and Mass Resolving Power for Peak Assignment in Top-down MS

• Jeffrey Agar (Northeastern University)

3:30 – 3:50 PM Advancing Top- and Middle-Down Antibody Analysis Using Simulated FTMS Datasets

• Yury Tsybin (Spectroswiss)

3:50 – 4:05 PM Computational Methods in Top-down Proteomics for Proteoform Analysis

• Kyowon Jeong (Korea University)

4:05 – 4:20 PM TDAuditor Assesses Deconvolution Quality for the Blood Proteoform Atlas

• David Tabb (Vanderbilt University)

4:20 – 4:40 PM Open Science Practices for Faster Development of Top-Down Proteomics

• Juan Antonio Vizcaino (EMBL-EBI)

4:40 – 4:50 PM Break

4:50 – 6:00 PM Minimum Information Describing A Proteoform (MIDAP) / Proteoform Atlas Compendium System (PACS)

7:00 – 9:00 PM Conference Dinner

Thu, August 28

8:30 – 8:50 AM Enabling High-Throughput Proteoform Analysis via Gel-Based Sample Pre-Fractionation with PEPPI-SP3

• Nobuaki Takemori (University of Tokyo)

8:50 – 9:05 AM Characterization of Proteoforms of Intact Proteins by CE-MS and LC-CE-MS

• Christian Neusüß (Aalen University)

9:05 – 9:20 AM Impact of Sample Preparation Methods on Proteoform Identification by Top-down Proteomics

• Andreas Tholey (University of Kiel)

9:20 – 9:35 AM Homogenization of Tissues via Picosecond-infrared Laser (PIRL) Ablation

• Hartmut Schlüter (University Medical Center Hamburg-Eppendorf)

9:35 – 9:50 AM Comparison of RP-LC with CE for Histone Analysis

• Ansgar Poetsch (Ruhr University Bochum)

9:50 – 10:20 AM Coffee Break

10:20 – 10:40 AM Advances in Orbitrap Mass Spectrometry for Top-down Analysis

• Alexander Makarov (Thermo Fisher Scientific)

10:40 – 11:00 AM Exploring Spatial Top-Down Proteomics

• Ljiljana Paša-Tolić (Pacific Northwest National Laboratory)

11:00 – 11:15 AM Exploring the Effects of Isotope Depletion on Proteins by Native Mass Spectrometry and Cryo-EM

• Anjusha Mathew (University of British Columbia)

11:15 – 11:30 AM Discovering the ‘Negative’ Side of the Proteomic Landscape with Top-down Mass Spectrometry

• Rafael Melani (CNRS)

11:30 – 11:45 AM Glycoproteomics Based on Deep Learning and Data Independent Acquisition

• Liang Qiao (Shanghai Institute of Materia Medica)

11:45 AM – 12:00 PM High Resolving Power Meets Proton Transfer Charge Reduction: Unlocking New Depths in Intact Protein Characterization

• Cynthia Nagy (Thermo Fisher Scientific)

12:00 – 1:00 PM Lunch Break

1:00 – 1:45 PM Poster Session 2

1:45 – 2:05 PM Top-Down Proteomics of the Heart: Decoding Cardiac Proteoforms for Precision Medicine

• Ying Ge (University of Wisconsin–Madison)

2:05 – 2:25 PM Dissecting the Proteoform Landscape of Prostate-Specific Antigen: Intact, Bottom-Up, and Glycomic Perspectives

• Guinevere Lageveen-Kammeijer (University of Groningen)

2:25 – 2:40 PM Spatial Phosphoproteomic Profiling Reveals Regional Functional Heterogeneity in the Murine Heart

• Ling Lin (University of Wisconsin–Madison)

2:40 – 2:55 PM A Top-down Hybrid MS Approach Captures Extent and Dynamics of Simultaneous Phosphorylation Events in AMP-Activated Kinase Complex

• Boris Krichel (University of Bonn)

2:55 – 3:05 PM Spatially Resolved Proteoform Mapping in Alzheimer’s Disease Brain Tissues

• Yue Sun (Columbia University)

3:05 – 3:15 PM Top-down Proteomics Deciphers Cardiac Proteoform Landscape in Phospholamban R14del Cardiomyopathy for Precision Medicine

• Holden Rogers (University of Wisconsin–Madison)

3:15 – 3:25 PM MALDI MS-Based Rapid Antimicrobial Susceptibility Prediction

• Jia Yi (Shanghai Jiao Tong University)

3:25 – 3:55 PM Coffee Break

3:55 – 4:15 PM Deciphering Biotherapeutic Biotransformations with Top-Down Mass Spectrometry

• Julia Chamot-Rooke (Institut Pasteur)

4:15 – 4:35 PM Functional and Structural Characterization of Antibodies by Native-Mode Affinity Separation-, Middle-Up, and Top-Down Mass Spectrometry

• Manfred Wuhrer (Leiden University Medical Center)

4:35 – 4:50 PM AiDA Accelerates Top-Down and Middle-Down MS Data Analysis Across Multiple Antibody Variants

• Francois Griaud (Thermo Fisher Scientific)

4:50 – 5:05 PM Enhanced Usage of Top-Down Data for De Novo Sequencing of Antibodies

• Kira Vyatkina (Protein Metrics Inc.)

5:05 – 5:20 PM Mass Spectrometric ITEM-FOUR Analysis Reveals Coding SNPs in Human Cardiac Troponin T That Evade Detection by ELISA

• Michael Glocker (University of Rostock)

5:20 – 5:50 PM Poster Awards and Farewell

Speakers

• Jeffrey Agar (Northeastern University, Bouvé College of Health Sciences)
• Julia Chamot-Rooke (Institut Pasteur)
• Paul Danis (Consortium for Top-Down Proteomics)
• Ying Ge (University of Wisconsin-Madison)
• Albert Heck (Utrecht University)
• Kyowon Jeong (Universität Tübingen)
• Neil Kelleher (Northwestern University)
• Guinevere Lageveen-Kammeijer (University of Groningen)
• Joseph A. Loo (University of California)
• Michal Sharon (Weizmann Institute of Science)
• Ole Nørregaard Jensen (University of Southern Denmark)
• Dimitris Papanastasiou (Fasmatech)
• Ljiljana Paša-Tolić (Pacific Northwest National Laboratory (PNNL))
• Lloyd Smith (University of Wisconsin-Madison)
• Nobuaki Takemori (Ehime University School of Medicine)
• Yury O. Tsybin (Spectroswiss)
• Charlotte Uetrecht (University of Lübeck, CSSB Centre for Structural Systems Biology, Deutsches Elektronen Synchrotron DESY)
• Juan Antonio Vizcaino (EMBL-EBI)
• Manfred Wuhrer (Leiden University)
• Mowei Zhou (Zhejiang University)

Short Courses

To sign up for the following short courses please click here and register.

Short Course 1: Top-Down Proteomics

Monday 25.08.2025 (9 am – 5 pm) & Tuesday 26.08.2025 (9 am – 1 pm)

This 2-day short course will give an overview about techniques and applications in top-down proteomics, proteoform research and biopharma, held by leading scientists in the field: Neil Kelleher,  Andreas Tholey, Julia Chamot-Rooke, Kyowon Jeong, Yury O. Tsybin and Hartmut Schlüter.

Program of the course:

• What are proteoforms and why are they important ?
• Sampling of tissues for proteoform analysis
• Liquid chromatography for proteoform fractionation
• Top-down proteomics – basic concepts
• Sample preparation for top-down proteomics 
• Mass spectrometry of intact proteins
• Fragmentation of proteoforms
• Top-down-proteomics data analysis - Introduction
• Applications: Analysis of therapeutic proteins in bio-pharma
• Applications: Disease-associated Proteoforms
• Short Course 2: Dissecting the impact of deconvolution on top-down identification

Friday 29.08.2025 (9 am – 1 pm)

This 1-day short course will explore the impact of deconvolution in the identification process, comparing Xtract, TopFD, and FLASHDeconv on the same input data.  Speakers will include Kyowon Jeong (University of Tuebingen) and David Tabb (University Medical Center of Groningen).  Participants will carry out analyses on their own laptops; note that either Microsoft Windows or Linux is necessary for TopPIC Suite support.  The software tools will be demonstrated via their GUIs.  Prior experience with programming languages is unnecessary.

Theme I: Assessing the degree of variation among deconvolution engines

Participants will deconvolve provided experiments via TopFD and FLASHDeconv on their own computers.  They will then analyze the msAlign outputs (as well as a provided MGF file from ProSight PD) in the TDAuditor quality tool.  A Jupyter Notebook will then visualize the variation in these deconvolution outputs.

Theme II: Detecting deconvolution impact on identifications

Participants will conduct a uniform TopPIC search on the deconvolution outputs.  A Jupyter Notebook will guide them through the resulting PrSMs (Proteoform-Spectrum Matches), revealing areas of agreement and disagreement stemming from the deconvolution process.

Bruker Daltonics Factory Tour

Register for a special behind-the-scenes tour of the Bruker Daltonics headquarters, where innovation in mass spectrometry and proteomics comes to life.

Register now

Register now to secure your place on this exclusive tour! 

What to expect:

• A guided tour of our state-of-the-art mass spectrometer production 
  Insights into the development of cutting-edge technologies like timsOmni™ and MRMS 
• A relaxed networking lunch with fellow symposium attendees

Event Details:

• Date: Friday, August 29, 2025, 8:45 am CEST
• Departure: Morning bus transfer from Von-Melle-Park 4, 20146 Hamburg, Germany
• Return: Early afternoon transfer back to Hamburg 
• Lunch: Light refreshments and lunch included

The tour is free of charge! Seats are limited and available on a first-come, first-served basis.

Venue

We are excited to host you at the University of Hamburg, located in one of Germany’s most vibrant and culturally rich cities.

The University of Hamburg, founded in 1919, is one of Germany’s leading research institutions and offers a broad range of academic disciplines. With a strong emphasis on interdisciplinary collaboration, the university hosts a variety of events, conferences, and academic exchanges that bring together scholars and practitioners from around the world.

The campus is located in the heart of Hamburg, making it an ideal place to connect academic pursuits with the city’s dynamic culture and history.

We look forward to welcoming you to the University of Hamburg!