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Postdoc Position in Computational Antigen Discovery – Utrecht University, Netherlands (Mass Spectrometry-Based Immunopeptidomics & Proteogenomics)

Postdoc position

8/10/2026

Utrecht University is offering a Postdoctoral Researcher position in Computational Antigen Discovery within the Department of Pharmaceutical Sciences, Faculty of Science. This is an excellent opportunity for a highly motivated and experienced computational biologist/bioinformatician interested in mass spectrometry-based immunopeptidomics, proteogenomics, antigen discovery for cancer immunotherapy, and AI/ML-driven multi-omics integration.

Position Snapshot

  • Institution: Utrecht University, Faculty of Science, Department of Pharmaceutical Sciences, Utrecht, Netherlands

  • Research Group: Dr. Marino’s group (specialized team focusing on discovery of previously unidentified antigens for immunotherapies through MS-based proteomics and immunopeptidomics)

  • Level: Postdoctoral Researcher (full-time, 36–40 hours per week)

  • Funding: Fully funded postdoctoral position through Utrecht University

  • Research areas:

    • Mass spectrometry (MS)-based proteomics and immunopeptidomics data analysis

    • Computational antigen discovery for cancer immunotherapy

    • Proteogenomics and multi-omics data integration (genomics, transcriptomics, ribosomal profiling, proteomics, immunopeptidomics)

    • AI/ML applications for prioritizing disease-specific targets

    • Development of scalable bioinformatics pipelines for antigen identification, quantification, and validation

  • Collaboration: Close collaboration with partners at Princess Maxima Center and other multidisciplinary teams

  • Start date: As soon as possible / by mutual agreement

  • Contract duration: Initially 1 year (with possibility of extension)

  • Application deadline: 31 August 2026

  • Application portal: Utrecht University online application system – https://www.uu.nl/en/organisation/working-at-utrecht-university/jobs/postdoc-position-in-computational-antigen-discovery

  • Application fee: None

  • Contact: For more information, contact Celine Miedema at t.c.miedema@uu.nl


About the Research Project

At Utrecht University, a specialized team focuses on the discovery of previously unidentified antigens for immunotherapies through mass spectrometry (MS)-based proteomics and immunopeptidomics. The group develops and applies state-of-the-art bioinformatics workflows for antigen identification, quantification, and validation, with direct applications in cancer immunotherapy and next-generation vaccine-based therapies.

The appointed Postdoctoral Researcher will play a central role in advancing the group’s research through the development and application of cutting-edge computational methods. The position offers close collaboration with experimental researchers, clinicians, and computational scientists at Utrecht University, Princess Maxima Center, and other partner institutions.

Key research activities include:

  • Developing and maintaining scalable pipelines for mass spectrometry (MS)-based proteomics and immunopeptidomics data analysis (DDA, DIA, PRM)

  • Designing integrative frameworks combining genomics, transcriptomics, ribosomal profiling and proteomics datasets for proteogenomics analyses

  • Developing and maintaining high-quality pipelines for processing and visualizing large-scale proteogenomics, MS-based immunopeptidomics/proteomics data

  • Ensuring reproducibility and scalability of workflows using modern workflow tools (e.g., Nextflow, Snakemake, CWL, etc.)

  • Applying AI/ML techniques to organize and merge multi-omics data for prioritizing disease-specific targets

  • Implementing antigen data analysis and discovery processes, including non-canonical HLA-bound peptide discovery pipelines, binding predictions, and in silico immunogenicity predictors

  • Contributing to scientific publications, grant writing, and presentations at international conferences

  • Collaborating with internal and external groups to develop new analysis pipelines tailored to immunopeptidomics experiments

  • Staying at the forefront of scientific advances in mass spectrometry-based immunopeptidomics/proteomics, including software and new methodologies

  • Taking the lead in developing new ideas and initiatives that advance the group’s research

This project combines computational biology, bioinformatics, mass spectrometry, proteogenomics, and AI/ML to address fundamental questions about antigen discovery and its applications in cancer immunotherapy and vaccine development.

Funding and Financial Support

Selected candidates will receive a fully funded postdoctoral position with the following core features:

  • Contract type: Full-time employment (36–40 hours per week), initially for 1 year with possibility of extension

  • Salary level: Gross monthly salary between €3,546 and €5,538 (salary scale 10 under the Collective Labour Agreement for Dutch Universities, CAO NU), depending on qualifications and experience

  • Benefits:

    • 8% holiday pay

    • 8.3% year-end bonus

    • Pension insurance with ABP (Utrecht University takes care of approximately 70% of the monthly contribution)

    • 100% public transport reimbursement

    • Reimbursement of €0.18 per km for commuting by car (up to a max. of 40 km one way) or support for cycling/foot commuting

    • Access to the newest and most advanced mass spectrometry instruments and computing infrastructures

    • Professional development opportunities, training, and access to university facilities

  • Research support: Access to state-of-the-art MS instruments, high-performance computing infrastructure, and funds for conference travel, research visits, and collaboration, as per Utrecht University norms

This funding model makes the position accessible to both Dutch and international candidates, provided they meet the eligibility and enrolment requirements.

Who Should Apply

This position is ideal for candidates with a strong background in bioinformatics, computational biology, mass spectrometry-based proteomics/immunopeptidomics, or related computational fields, and a clear interest in antigen discovery, cancer immunotherapy, and multi-omics data integration.

Academic Background

Applicants should hold a PhD in bioinformatics, computational biology, or a closely related field (e.g., computational genomics, proteomics, systems biology, biomedical informatics).

Required Qualifications and Experience

Ideal candidates will demonstrate:

  • Proven experience analysing different mass spectrometry-based immunopeptidomics/proteomics data (i.e., DDA, DIA, PRM) with platforms such as FragPipe, Peaks, Spectronaut, MaxQuant, Skyline or equivalent tools

  • Solid background in state-of-the-art packages and analysis pipelines in mass spectrometry-based immunopeptidomics

  • Experience with non-canonical HLA-bound peptide discovery pipelines, binding predictions and other in silico tools (e.g., immunogenicity predictors and/or HLA-peptide-TCR binding, etc.)

  • Experience in multi-modal data integration for prioritizing disease-specific targets: combining quantitative multi-omics approaches (e.g., RNA-seq, Ribo-seq, proteomics, immunopeptidomics)

  • Strong programming skills in Python, R, or similar languages

  • Self-starting and collaborative attitude

  • Excellent written and spoken English (Dutch is not required but can be helpful for daily life in Utrecht)


Preferred Qualifications and Experience

  • AI/ML applications: applying machine learning or AI to integrate, discover and prioritize disease-specific targets across omics

  • Experience with workflow management tools (e.g., Nextflow, Snakemake, CWL)

  • Experience in cancer immunology, immunopeptidomics, or related translational research

  • Track record of scientific publications in peer-reviewed journals

Prior research experience (e.g., postdoctoral work, PhD thesis on proteomics, immunopeptidomics, computational antigen discovery, or related topics) and publications in relevant venues are strongly recommended.

Application Materials

Applications must be submitted online only via the Utrecht University online application system. Incomplete or late applications will not be considered.

Required documents typically include:

  • Letter of motivation explaining your motivation, relevant background, and fit with the computational antigen discovery project and research group

  • Curriculum Vitae (CV) detailing education, research experience, technical skills, and any publications or relevant projects

  • Contact details of at least two references (names, telephone numbers, and email addresses)

All documents should be uploaded in the formats specified in the online application system. Applications that do not meet the formal requirements or are submitted after the deadline will not be considered.

How to Apply (Step-by-Step)

  1. Review the official job posting and project description

    • Read the full job posting on the Utrecht University website to understand the research theme, requirements, and application instructions.

    • Note the position title: “Postdoc Position in Computational Antigen Discovery” and research group: Dr. Marino’s group.

  2. Prepare your application documents

    • Update your CV to highlight relevant coursework, projects, and skills in bioinformatics, computational biology, mass spectrometry, proteomics, and AI/ML.

    • Draft a targeted letter of motivation that connects your background to the specific project (computational antigen discovery for cancer immunotherapy), mentions any relevant lab or computational experience, and explains your motivation for pursuing a postdoc in this area.

    • Confirm your referees’ contact details (names, telephone numbers, and email addresses) and ensure they are willing to provide reference letters if contacted.

  3. Access the online application portal

  4. Complete the online form and upload documents

    • Fill in all required personal and academic details.

    • Upload your letter of motivation, CV, and referee contacts in the specified formats (usually PDF).

    • Double-check that all files are correctly attached and readable before final submission.

  5. Submit before the deadline

    • Ensure your application is submitted no later than 31 August 2026.

    • The system will not accept applications after the closing date; late submissions are not considered.


Selection Process and Timeline

The recruitment process typically involves:

  • Initial evaluation: Dr. Marino and the research group review all submitted applications based on academic profile, research fit, technical skills, and motivation.

  • Shortlisting and interviews: Shortlisted candidates are invited for interviews (usually online or on-site) to discuss their background, research interests, and fit with the project and team.

  • Final selection and offer: Successful candidates receive formal offers and instructions for contract signing and onboarding at Utrecht University.


Key dates from the official call and summaries are:

  • Application deadline: 31 August 2026

  • Employment start: As soon as possible / by mutual agreement

  • Contract duration: Initially 1 year (with possibility of extension)


Why This Opportunity Stands Out

This postdoc position offers a rare combination of:

  • Fully funded postdoctoral contract with competitive Dutch salary (€3,546–€5,538 gross/month, scale 10) and excellent employee benefits (holiday pay, year-end bonus, pension, transport reimbursement)

  • A clearly defined, high-impact research project on computational antigen discovery for cancer immunotherapy, with direct relevance to translational medicine, precision oncology, and next-generation vaccine development

  • Interdisciplinary collaboration with leading groups at Utrecht University, Princess Maxima Center, and other partner institutions, offering exposure to cutting-edge MS instruments, multi-omics data, and a strong publication record

  • A vibrant research environment in Utrecht, with access to excellent research facilities, state-of-the-art computing infrastructure, and a strong network of computational biologists, immunologists, and clinicians


For candidates passionate about computational biology, mass spectrometry-based proteomics/immunopeptidomics, and antigen discovery for cancer immunotherapy, this is an excellent opportunity to pursue a high-impact postdoc at one of Europe’s leading research universities.

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