Postdoc in Computational Palaeoproteomics

Københavns Universitet; København; On-site; DKK 520,000 - 640,000; Full time

Job summary

University of Copenhagen's Globe Institute invites applications for a 30-month postdoc in computational palaeoproteomics starting 1 November 2026. You will develop scalable computational workflows and contribute to mass-spectrometry data analysis.

The role blends research software engineering with analysis of DDA and PRM data from ancient proteins, collaborating with archaeologists, proteomics scientists and external partners.

Qualifications

• PhD in palaeoproteomics, proteomics, bioinformatics, computational biology, archaeological science or related field.
• Experience with computational analysis and interpretation of LC-MS/MS data.
• Experience with DDA and PRM analyses using MaxQuant or Skyline.
• Proficiency in R, Python, and Bash; workflow automation in Linux/HPC.
• Experience developing database-backed software or web apps (Java/Spring, Vaadin, PostgreSQL).
• Experience with relational database design and traceability of samples/workflows.
• Excellent written and spoken English.

Responsibilities

• Develop, maintain and deploy scientific software and automated workflows for palaeoproteomics.
• Integrate order and sample metadata with analysis status and results.
• Automate reproducible processing on local and HPC infrastructure.
• Analyse DDA data using database-search and de novo approaches.
• Analyse targeted PRM data and improve classification methods.
• Document software and workflows; contribute to manuscripts and grants.
• Collaborate with laboratory researchers and external partners.
• Teach or supervise as needed.

Skills

Computational palaeoproteomics

Mass-spectrometry data analysis

Scientific software development

R and Python programming

Java programming

Workflow automation

Linux / HPC

Database-backed software

Documentation and reporting

Team collaboration

English proficiency

Education

PhD in palaeoproteomics, proteomics, bioinformatics, computational biology or related

Tools

MaxQuant

Skyline

R

Python

Java

Spring

Vaadin

PostgreSQL

Linux

Job description

Postdoc in Computational Palaeoproteomics

Globe Institute, Faculty of Health and Medical Sciences

University of Copenhagen

We are looking for a highly motivated and dynamic postdoc for a 2.5 year (30 months) fixed term and full-time position starting on the 1 November 2026, or immediately thereafter.

The Palaeoproteomics research group led by Professor Enrico Cappellini is looking for a highly competent, motivated, and dynamic postdoc,with demonstrated experience in computational palaeoproteomics, mass-spectrometry data analysis and scientific software development. The position will contribute to the development of high-throughput computational infrastructure for palaeoproteomics and targeted biological sex identification. It will support reproducible processing, quality control and interpretation of mass-spectrometry data and connect customer-facing sample management with traceable analytical workflows and research outputs.

Our research
The molecular identification of fossil taxa and reconstruction of the phylogenetic relationships connecting them remain central challenges in evolutionary research. The Palaeoproteomics group develops and applies mass-spectrometry-based methods to recover ancient protein sequences beyond the limits of ancient DNA preservation. The work will combine research-software engineering with computational analysis of DDA and PRM data from ancient and highly degraded protein samples. Close collaboration with laboratory scientists, archaeologists and external partners is central to the position. The candidate will work to develop scalable palaeoproteomic methods and high-throughput targeted proteomics. The successful candidate will join an interdisciplinary environment spanning palaeoanthropology, evolutionary biology, archaeology and mass spectrometry. The environment provides access to the University of Copenhagen's Mjolnir high-performance computing cluster, advanced proteomics expertise and active national and international collaborations.

Your job
The postdoc will develop, maintain and deploy scientific software and automated workflows for palaeoproteomics. Responsibilities include integrating order and sample metadata with analysis status and results; automating reproducible R-, Python- and Java-based processing on local and HPC infrastructure; analysing DDA data using database-search and de novo approaches; analysing targeted PRM data; improving and validating classification methods; documenting software and workflows; contributing to manuscripts and grant or translational activities; and participating in teaching and supervision.

Profile
We are looking for a collaborative and independent researcher who combines strong computational proteomics expertise with practical software-engineering skills. The candidate should be able to translate research requirements into reliable workflows and communicate results across disciplinary boundaries.

Essential experience and skills:

• A PhD in palaeoproteomics, proteomics, bioinformatics, computational biology, archaeological science or a closely related field.
• Experience with computational analysis and interpretation of LC-MS/MS proteomics data.
• Experience with both data-dependent acquisition and targeted PRM analysis, using MaxQuant, Skyline or comparable tools.
• Proficiency in R or Python and Bash, including workflow automation in Linux or HPC environments.
• Experience developing database-backed scientific software or web applications using Java/Spring, Vaadin and PostgreSQL, or equivalent technologies.
• Experience with relational database design, sample and workflow traceability, and structured results management.
• Experience with reproducible software practices, including version control, testing, containerisation and continuous integration/deployment.
• Ability to document and communicate computational methods clearly in publications, technical documentation and presentations.
• Ability to work effectively with laboratory researchers, archaeologists, bioinformaticians and external collaborators.
• Strong organisational skills and the ability to deliver independent work to agreed deadlines.
• Excellent spoken and written English.

Desirable experience and skills:

• Experience with high-throughput targeted proteomics for biological sex identification from tooth enamel.
• Experience developing R Shiny applications and converting interactive analyses into unattended Rscript workflows.
• Experience with de novo peptide sequencing tools, such as InstaNovo, and comparison with database-search results.
• Experience validating classifications using independent evidence, such as aDNA results and manual spectrum inspection.
• Experience deploying secure, role-based production systems for internal or external users.
• Experience teaching or supervising palaeoproteomics, proteomics data analysis or research software.
• Experience contributing to successful grant applications, translational research or commercialisation activities.

Place of employment
The place of employment is at the Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen. We offer creative and stimulating working conditions in dynamic and international research environment. The position provides access to computational infrastructure, including the Mjolnir HPC cluster, a dedicated windows server, and close interaction with the Institute's palaeoproteomics laboratories and mass-spectrometry research environment.

About Globe Institute
The Globe Institute is part of the Faculty of Health and Medical Sciences at the University of Copenhagen. The Institute’s main purpose is to address basic scientific questions through interdisciplinary approaches. The institute operates at the intersection of natural and medical sciences and the humanities. Information on the institute can be found at: www.globe.ku.dk .

Globe Institute is committed to creating an inclusive and diverse environment where employees and students can belong and thrive. See website for more information. All qualified applicants will receive full consideration. Candidates who, through their research, teaching, and/or service, contribute to diversity and competencies of our Institute are encouraged to apply. The University of Copenhagen strives to offer a family friendly and flexible working environment with a sustainable balance between work- and private life, including parental leave schemes (up to 47 weeks for both parents) and up to six weeks of paid holidays per year. Researchers that have not been tax liable in Denmark for the last 10 years can apply for a special (reduced) tax scheme. The university offers a variety of services for international researchers and accompanying families.

Terms of employment
The position is covered by the Memorandum on Job Structure for Academic Staff.

Terms of appointment and payment accord to the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State.

There will be an opportunity to negotiate supplements based on qualifications. You can read more about salary levels in the state sector www.loenoverblik.dk (in Danish).

Foreign applicants may find this link useful: www.ism.ku.dk (International Staff Mobility).

The University of Copenhagen wish to reflect the diversity of society and encourage all qualified candidates to apply regardless of personal background.

Part of the InternationalAllianceof Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.

Contact: University of Copenhagen
[e-mail]