Spatial Proteomics

Infrastructure Unit

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.


SciLifeLab Staff:

Charlotte Stadler, Head of Unit

Carolina Oses Sepulveda, Researcher and lab manager

Eleanor O´Roberts, Researcher

Anna Bäckström, Senior Research engineer

Pranauti Panshikar, Research engineer

Johan Thorsson, Research engineer

Maria Lung, Master Thesis Student

Associated unit staff:

Tony Ullman, PhD Student

Ashik Jawahar-Deen, Post-doc

Spatial Proteomics

Our unit provides service in highly multiplexed immunofluorescence (up to 40 markers) of tissue sections. As one of a few labs in Europe we offer service using the Phenocycler platform (previosuly known as CODEX)). The Phenocycler technology is compatible for fresh frozen (FF) and paraffin embedded (FFPE) tissue sections from mouse and human. We offer the complete list of pre-conjugated antibodies available from Akoya Biosciences and the list of available antibodies can be found here. In addition, we can perform in house custom antibody conjugation for essential targets of your project.

We also offer multiplexing using the COMET instrument from Lunaphore. This is based on sequential IF using primary off the shelf antibodies. Depending on your need and specific project we will discuss what methods for multiplexing that is the most suitable for each project.

The unit also enables researchers to access the resources and expertise from the Human Protein Atlas ( and the primary aim is to do full service immunofluorescence projects at moderate to high-throughput level in cell lines. Based on the resource of more than 25,000 antibodies and a panel of >30 different human cell lines, we offer a unique possibility to explore hundreds of protein targets at subcellular level under various cellular states and conditions.


We perform everything from project design, sample preparation and imaging to give you as good results as possible. We share infrastructure and resources with the Human Protein Atlas and this include a proteome wide library of antibodies that can be used in tailor made projects to answer specific biological questions.

Proposed projects are assessed and prioritized according to the following model

Initial screen of project by unit:

  1. Technical feasibility (yes/no)
  2. Capacity requested for the project (classification: small/medium/large)

Project prioritization is based on:

  1. Scientific potential
  2. Significance of unit specific technique for project
  3. Supporting preliminary data
  4. Supports unit development (competence and techniques)
  5. Feasibility of time lines


  • Cell type distribution and interactions in tissue samples
  • High-throughput subcellular profiling of protein targets in single cells using 4-plex immunofluorescence
  • Targeted phenotypic screening (elucidate mechanism of action for drugs)

Here are a few examples of previous projects:

  1. Spatial mapping of the host cell proteins upon SARS-CoV2 infection (screening of 700 proteins for identification of potential druggable targets)
  2. Explore the effect of a small molecule/substance on a particular organelle, family of proteins or proteins within a defined pathway.
  3. Screen for proteins co-localizing with a defined marker in different cellular conditions like autophagy, serum starvation or hypoxia.
  4. Confirm data from mass spectrometry experiments, such as translocation of proteins
  5. Evaluation of immune cell infiltration in muscle biopsies from diabetic patients before and after physical exercise
  6. Validate knock-out cell lines and antibodies by evaluation of fluorescence signal reduction and quantitative image analysis


  • Phenocycler Fusion platform, enabling highly multiplexed imaging (>30) at single cell level in tissue sections
  • COMET – automated sequential immunofluroescence
  • LabSat – automated stainer of single slides
  • Antibodies. 25,000 ICC validated antibodies from the Human Protein Atlas project.
  • Liquid handling. TECAN FREEDOM EVO 150 pipetting robots. One TECAN Fluent 480.

Using the unit

Please send us an email with questions, suggestions or project proposals using the contact emails below. We will get back to you shortly after to schedule a meeting for further discussions if applicable.

Last updated: 2024-01-09

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