Computational Proteomics Scientist

Are you a motivated computational scientist passionate about developing algorithms for cutting-edge proteomics? We are looking for an enthusiastic Computational Proteomics Scientist to join the Proteomics and Metabolomics Team at the European Bioinformatics Institute (EMBL-EBI). The successful candidate will contribute to the development of algorithms, computational resources, and community standards for single-cell proteomics, working at the interface of data science, software engineering, and biological discovery.

Our team is responsible for the development and maintenance of world-leading proteomics resources, including PRIDE, a founding member of the ProteomeXchange Consortium, which captures and disseminates large-scale proteomics data from the global scientific community. We are also major contributors to international standardisation efforts through the Proteomics Standards Initiative (PSI). Single-cell proteomics is an emerging and rapidly evolving field, generating complex, sparse, and large-scale datasets. You will play a key role in designing scalable computational methods and standards to support robust analysis, reproducibility, and FAIR data sharing for next-generation proteomics experiments.

Your Role

• Design and develop algorithms for single-cell proteomics data analysis, including peptide/protein quantification, normalisation, missing value handling, batch correction, and quality control.
• Develop scalable and high-performance software components in Python and C++ for processing large-scale and high-dimensional proteomics datasets.
• Contribute to machine learning and deep learning approaches for proteomics data analysis, including representation learning, denoising, feature selection, and integrative multi-omics analysis.
• Participate in the definition and implementation of community data standards, formats, and APIs for single-cell proteomics under the umbrella of the Proteomics Standards Initiative.
• Work closely with experimental scientists and software engineers to integrate algorithms into production-ready workflows, databases, and cloud-based infrastructures.
• Support the transformation of proteomics resources into AI-ready datasets, enabling downstream use by advanced analytics and large-scale machine learning systems.
• Collaborate with other EMBL-EBI teams and international partners to integrate single-cell proteomics data with resources such as Expression Atlas and UniProt.

You Have

• A strong background in computational proteomics, bioinformatics, computer science, or a related quantitative discipline, with typically 3+ years of relevant research or industry experience.
• Strong experience in mass spectrometry-based proteomics, ideally including single-cell or low-input proteomics.
• Proven experience developing algorithms for proteomics data analysis.
• Excellent programming skills in Python and C++, with a focus on performance, maintainability, and reproducibility.
• Experience with machine learning and/or deep learning frameworks (e.g. PyTorch, TensorFlow, JAX, scikit-learn).
• Solid understanding of statistical methods for high-dimensional and sparse biological data.
• Experience working with large-scale datasets, including efficient I/O and memory-aware data processing.
• Proficiency with version control systems such as Git.
• Ability to work independently, manage multiple priorities, and communicate results clearly in an international environment.

You May Also Have

• Experience with proteomics data formats and standards (e.g. mzML, mzIdentML, mzTab, Parquet-based formats).
• Familiarity with high-performance computing (HPC), GPU acceleration, or parallel computing.
• Experience with workflow systems (e.g. Nextflow) and containerised environments (Docker, Singularity).
• Knowledge of cloud-based infrastructures and scalable data processing frameworks.
• Interest in FAIR data principles, open science, and community-driven standardisation.
• Experience integrating proteomics data with other omics modalities (e.g. transcriptomics, metabolomics).

Contract length: This position is project-based and offered as a fixed-term contract until 04 January 2029.

Salary: Grade 5, monthly starting salary at £3,303 – £3,638 per month after tax but excluding pension and insurance contributions. Plus, generous benefits.

Next Steps: This vacancy will be advertised from Tuesday, 20th January with a scheduled closing date of Tuesday, 3rd February. We welcome your application as soon as possible. Please provide an up-to-date CV and cover letter.

Why join us

At EMBL-EBI you can apply your talent and passion to accelerate science and tackle some of humankind's greatest challenges. EMBL-EBI, part of the European Molecular Biology Laboratory, is a worldwide leader in the storage, analysis and dissemination of large biological datasets. We provide the global research community with access to publicly available databases and tools which are crucial for the advancement of healthcare, food security, and biodiversity.

Enjoy Lots Of Benefits

• Financial incentives: Monthly family, child and non-resident allowances, annual salary review, pension scheme, death benefit, long-term care, accident-at-work and unemployment insurances.
• Flexible working arrangements – including hybrid working patterns.
• Private medical insurance for you and your immediate family (including all prescriptions and generous dental & optical cover).
• Generous time off: 30 days annual leave per year, in addition public holidays.
• Relocation package including installation grant (if required).
• Campus life: Free shuttle bus to and from work, on-site library, subsidised on-site gym and cafeteria, casual dress code, extensive sports and social club activities (on campus and remotely).
• Family benefits: On-site nursery, 10 days of child sick leave, generous parental leave, holiday clubs on campus and monthly family and child allowances.
• Benefits for non-UK residents: Visa exemption, education grant for private schooling, financial support to travel back to your home country every second year and a monthly non-resident allowance.

For detailed information please visit our employee benefits page here.

What else you need to know

• International applicants: We recruit internationally and successful candidates are offered visa exemptions.
• Diversity and inclusion: At EMBL, we believe that diverse teams drive innovation and scientific excellence. We encourage applications from candidates of all genders, identities, nationalities and/or any other diverse backgrounds.

How to apply: To apply please submit a cover letter and a CV through our online system. Applications will close at 23:59 CET on the date shown below. We aim to provide a response within two weeks after the closing date.

Closing Date: 03 / 02 / 2026