Senior Mass Spectrometry Scientist (Deputy Head of Metabolomics)

Senior Mass Spectrometry Scientist (Deputy Head of Metabolomics)

Location: Munich, Germany ); Budapest, Hungary (2028-)

Organization: CMF, Lead Entity for the protecting.health Global Initiative

Type: Full-time

The Center for Molecular Fingerprinting (CMF, is an interdisciplinary, nonprofit research institution led by the 2023 Nobel Laureate in Physics Prof. Dr. Ferenc Krausz. The team comprises laser scientists, molecular biologists, medical doctors, engineers, and data analysts dedicated to advancing health monitoring and early disease detection.

As part of the H4H (Health for Hungary – Hungary for Health) and protecting,health global initiatives, we are collecting biofluid samples from thousands of volunteers over ten years across Hungary, Germany, and Hong Kong. We seek a Senior Mass Spectrometry Scientist to serve as Deputy Head of Metabolomics.

Key Responsibilities:

• Execute preventive maintenance (source cleaning, vacuum checks, calibrations, tuning) and maintain detailed service logs for all instruments.
• Diagnose and resolve hardware and performance issues (vacuum, pumps, ion optics, electronics, LC components); perform repairs when feasible.
• Coordinate vendor service (Waters) and manage spare parts, consumables, and service contracts; track costs and lead time critical inventory.
• Establish and monitor KPIs (uptime, failures, turnaround time, mass accuracy, sensitivity) and drive root‑cause analysis and continuous improvement.

Metabolomics platform leadership (Deputy Head of Metabolomics)

• Support the Head of Metabolomics in planning capacity, prioritizing projects, and coordinating day‑to‑day platform activities.
• Own the instrument operations schedule (runs, calibrations, service windows) to maximize uptime and throughput for human‑cohort studies.
• Develop, maintain, and enforce SOPs for instrument operation, maintenance, and quality assurance; ensure documentation is audit‑ready.
• Train and mentor scientists and technicians in best practices for Waters G3 operation, troubleshooting, and contamination prevention.

High‑throughput LC‑MS metabolomics for human biofluid samples

• Optimize and maintain robust LC‑MS methods for high‑throughput analyses (e.g., run time, carry‑over control, contamination management, stability).
• Design and implement QC strategies (pooled QCs, blanks, system suitability, drift monitoring) and define acceptance criteria for routine production.
• Work closely with sample preparation and automation teams to ensure smooth end‑to‑end workflows and rapid recovery from interruptions.
• Review system performance trends, investigate outliers, and communicate clear, actionable updates to stakeholders; contribute to reports and publications.

Required Qualifications & Experience

• MSc or PhD in analytical chemistry, biochemistry, pharmaceutical sciences, or a related field.
• ≥5 years of hands‑on experience in LC‑MS‑based metabolomics, including running high‑throughput studies on human biofluids.
• Strong hands‑on experience operating, maintaining, and troubleshooting Waters (UPLC and G3‑generation MS) systems; service/repair experience is a plus.
• Solid understanding of MS fundamentals (ion sources, vacuum systems, ion optics, calibration/lockmass, mass accuracy, sensitivity) and common failure modes.
• Demonstrated ability to lead in a matrix environment: training others, setting standards, and driving continuous process improvement.
• Excellent English language skills (written and spoken) for international collaboration and scientific reporting.

We offer

• A versatile range of work packages, including:
• Higher‑than‑usual cafeteria allowance.
• Private health insurance.
• 30 guaranteed annual vacation days.
• Professional training opportunities.
• Team activities and team‑building events.
• A dynamic work environment with the opportunity to engage in a rapidly evolving and innovative field.
• Long‑term opportunities alongside highly qualified and motivated professionals.
• An international work environment with professional development opportunities.
• A solution‑oriented atmosphere with the chance to contribute to the success of a dynamic and growing organization.

Application Information

• Short cover letter (max 2 pages) outlining your fit for the Senior Mass Spectrometry Scientist role.
• Send applications to:
• Subject line: Application - Senior Mass Spectrometry Scientist - CMF
• Application Deadline: 15 April 2026
• Applications will be reviewed on a rolling basis; the position may be filled before the deadline. Early applications are strongly encouraged.
• CMF reserves the right to close the advertisement as soon as suitable candidates have been identified.