Structural Proteomics

Infrastructure Unit


Simon Ekström D13, Lund

Recent user publications

The publications in this database are the result of research conducted at the units of SciLifeLab – both in user projects and technology development.


Simon Ekström, Head of Unit

Lotta Happonen, Senior research specialist

Lucas Hultgren, Research engineer

Filip Årman, Bioinformatician


Johan Malmström, Platform Scientific Director

Structural Proteomics

The Structural Proteomics infrastructure unit provides access to cutting-edge equipment and expertise, for analysis of protein interactions and conformational dynamics with mass spectrometry.

The unit is part of the Integrated Structural Biology (ISB) platform, which also includes The Swedish NMR Centre and is virtually linked to the SciLifeLab CryoEM unit. These platforms combined with close ties with other stakeholders in the field, such as MAX IV, ESS, PPS and ProLinC, ensures that our users can gain access to multiple sources of data, as scientific questions encountered in structural biology rarely are solved by one technique alone. 

Our aim is to provide:

  • An internationally competitive infrastructure that is accessible to all academic scientists in Sweden on an equal opportunities basis.
  • A training and educational framework with scientific meetings, practical workshops and training courses where researchers can become familiar with cutting-edge methods used in the field of structural biology.
  • Improved accessibility to advanced structural protein analysis technologies and integration of data obtained using complementary technologies, through the new ISB platform.

The Structural Proteomics unit is supported by SciLifeLab and as a part of the Swedish National Infrastructure for Biological Mass Spectrometry (BioMS) also by the Swedish Research Council and hosting universities.


The unit provides service for all aspects of structural proteomics, including project planning, sample preparation, data collection and data analysis. Current Hydrogen Deuterium Exchange (HDX) and Crosslinking Mass Spectrometry services and workflows are well established and available to all users;

  • Bottom-up HDX-MS to provide detailed information on protein dynamics and conformation, e.g. identification of disordered protein regions, protein-ligand interaction sites (epitope mapping).
  • Cross linking (XL-MS) experiments with a variety of cross linkers to determine topological arrangements in protein complexes and pinpoint where the protein domains interface.
  • Denovo Sequencing of monoclonal antibodies (New for 2023)
     Provides sequence verification, and allows for characterization of post-translational modifications to ensure antibody integrity and effectiveness.

Additional services (under development or available upon request)

  • Quantitative affinity purification MS
  • High resolution HDX-MS with ETD fragmentation
  • Top-down and middle down HDX-MS
  • Hands-on training, educational presentations

If you have questions regarding our technologies and methods e.g., how they could be applied to your scientific questions. Please feel free to contact us, we are available for counselling either in person of via Skype/Zoom, on short notice.


Currently users can get access to our HDX-MS or XL-MS services through the BioMS portal for project requests (green button below). Each project is evaluated and prioritized by the nodes according to preset criteria: feasibility, relevance, national importance and synergies with other infrastructures or partners. Please, label applications “HDX and Attention/contact: Simon Ekström”

Remember you are always welcome to contact us prior to submitting an application for a discussion, we are more than happy to talk about science and/or practical details!

If you have a scientific problem that needs to be addressed by use of multiple different structural biology technologies or doubts as to which method to start with, just let us know and we’ll set-up a joint meeting with representation from all relevant units.

Note; Industry users are very welcome, but be aware that cost is not subsidized and if secrecy is an issue contact us directly (not through the application portal).


LEAP HDX automation with 4 independently controlled temperature zones and an Ultimate 3000 LC, movable between our MS instruments.

Bruker timsTOF ion mobility MS (new 2021)

Thermo Scientific Orbitrap Eclipse Tribrid MS (new 2021)

Access to >10 other Orbitrap MS instruments on site

Visiting address

Structural proteomics, SciLifeLab and BioMS
Lund University

(Simon Ekström, room D1314B)
Klinikgatan 36, BMC D13
221 84 Lund

Last updated: 2023-12-01

Content Responsible: David Gotthold(