Proteomics Application Specialist (Special Consultant)

Background

The Proteomics Research Infrastructure (PRI) is a cutting-edge core facility specializing in mass spectrometry (MS)-based proteomics. PRI provides researchers with end-to-end support, including project consultation, automated sample preparation, mass spectrometry acquisition, and advanced data analysis.

Established within the Novo Nordisk Foundation Center for Protein Research (CPR) and now part of the Center for Core Facilities (CCF), PRI operates in an international, collaborative, and innovation-driven environment. English is the primary working language.

We are seeking an experienced Proteomics Application Specialist (Special Consultant) to support and further develop PRI's advanced proteomics applications, with a particular focus on post-translational modification (PTM) proteomics.

Job description

The Proteomics Application Specialist will be an integral member of the PRI team and will play a key role in the operation, development, and continuous improvement of PRI's advanced proteomics applications and service pipelines.

The position involves planning, performing, analyzing, and documenting a broad range of proteomics experiments, including global proteome profiling, interaction proteomics, PTM proteomics, and other specialized applications. A particular focus will be on the development, optimization, and implementation of workflows for the enrichment and quantitative analysis of protein post-translational modifications, including phosphorylation and other PTMs.

In addition to these specialized activities, the successful candidate will contribute to PRI's routine service operations, including sample preparation, LC–MS analysis, data processing, and quality control. The position also involves the development and implementation of robust, reproducible, and scalable laboratory workflows.

The successful candidate will work closely with the PRI team, particularly the Proteomics Service Manager, and will report directly to the PRI Director.

Key responsibilities

• Plan, execute, analyze, and document experiments across PRI's proteomics service pipelines, including global proteomics, interaction proteomics, PTM proteomics, and other specialized applications.
• Support and further develop PTM proteomics workflows, including sample preparation, enrichment, LC–MS acquisition, and quantitative data analysis.
• Develop, optimize, and validate methodologies for the enrichment and analysis of post-translationally modified peptides and proteins, particularly phosphoproteomics and other modification-specific applications.
• Perform sample preparation for a broad range of proteomics applications, including high-throughput and large-scale sample processing.
• Operate, maintain, troubleshoot, and optimize state-of-the-art LC–MS instrumentation and related proteomics technologies.
• Develop and optimize LC–MS acquisition methods, including data-dependent acquisition (DDA), data-independent acquisition (DIA), and multiplexed quantitative approaches.
• Perform proteomics data analysis using specialized software, including protein identification, quantification, PTM site localization, and interpretation of experimental results.
• Operate, maintain, and optimize automated sample preparation and liquid-handling platforms.
• Maintain comprehensive and accurate experimental documentation using electronic laboratory notebooks and project and sample management systems.
• Contribute to the development, validation, standardization, and continuous improvement of laboratory workflows.
• Support the implementation of scalable and reproducible processes to ensure high quality and efficiency across PRI's service activities.
• Collaborate with researchers, project partners, and PRI colleagues in an international and multidisciplinary environment.
• Contribute to the development of new applications and technologies relevant to PRI's research and service portfolio.
• Perform other relevant duties as required to support the activities and strategic development of PRI.

Qualifications

We are looking for a reliable, well-organized, and highly motivated scientist with a strong background in mass spectrometry-based proteomics who can work independently while contributing effectively to a collaborative and service-oriented team environment.

The position requires flexibility, accuracy, attention to detail, and a strong commitment to high-quality laboratory work, methodological development, and service delivery.

The ideal candidate will have

• A PhD in molecular biology, biochemistry, proteomics, analytical chemistry, or a related field.
• Extensive hands-on experience with state-of-the-art LC–MS-based proteomics, including operation, maintenance, troubleshooting, and method optimization of high-resolution mass spectrometry instrumentation.
• Demonstrated expertise in PTM proteomics, particularly phosphoproteomics, including practical experience with PTM enrichment strategies, LC–MS acquisition, and quantitative data analysis.
• Extensive practical experience with proteomics sample preparation and quantitative proteomics workflows, including global proteome profiling and other specialized proteomics applications.
• Demonstrated experience with the development, optimization, validation, and implementation of advanced proteomics methodologies and experimental workflows.
• Strong experience with data-dependent acquisition (DDA) and data-independent acquisition (DIA) methods, including the development and optimization of acquisition strategies.
• Advanced experience with proteomics data analysis using specialized software, including protein identification, quantification, and PTM site localization.
• Hands-on experience with automated liquid-handling platforms.
• Demonstrated ability to independently manage complex experimental projects, troubleshoot technical challenges, and ensure high analytical quality and reproducibility.
• Excellent organizational skills, strong computer literacy, and experience with electronic laboratory notebooks and laboratory or project management systems.
• Excellent oral and written communication skills in English, including the ability to communicate complex technical and scientific information effectively.

The following qualifications will be considered advantageous

• Experience with advanced quantitative PTM proteomics approaches, including TMT-based multiplexing and specialized fragmentation techniques such as ETD or EThcD.
• Hands-on experience with Thermo Fisher Orbitrap Tribrid and Orbitrap Astral platforms.
• Previous experience working in a proteomics core facility or other service-oriented research environment.

Employment conditions for the Proteomics Application Specialist (Special Consultant)

The employment is a fixed-term position until 30 June 2030, with the possibility of extension. The estimated start date is January 1, 2027. Working hours are 37 hours per week. The place of work is the Proteomics Research Infrastructure, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark.

Employment will be as Special Consultant (Staff Scientist) under The Circular on the Collective Agreement concerning Academics in the state sector concluded between the Danish Ministry of Finance and Akademikerne (the Danish Confederation of Professional Associations). There will be an opportunity to negotiate supplements based on qualifications. The employer will pay an additional 18.07% to your pension fund. You can read more about salary levels in the state sector www.loenoverblik.dk (in Danish).

Informal inquiries about the position can be addressed to the PRI Director, Michael Wierer; [email protected] . For more information on PRI visit: www.pri.ku.dk

To apply

Your application must be submitted in English. Only online applications will be accepted and must include:

• Motivation letter
• Curriculum vitae
• Copy of relevant diplomas

Please submit your application with the required attachments by clicking on "Apply for position" below.

Deadline for applications is November 6, 2026, 23:59 CET. Applications or attachments received after the deadline will not be considered.

The University of Copenhagen encourages all qualified candidates to apply, regardless of personal background.