Proteomics and Bioinformatics Scientist

Do you want to work for a world-renowned research institute that pushes the boundaries of biomedical science and health research? Right here in Montreal! At the Research Institute of the McGill University Health Centre (RI-MUHC), you can be part of an organization focused on scientific discovery and innovation in patient-centered medicine. Join us today and make a difference!

Job Description

RESEARCH INSTITUTE OF THE MUHC
The Research Institute of the McGill University Health Centre (RI-MUHC) is a world-renowned biomedical and hospital research centre. Located in Montreal, Quebec, the Institute is the research arm of the McGill University Health Centre (MUHC) affiliated with the Faculty of Medicine at McGill University. The RI-MUHC is supported in part by the Fonds de recherche du Québec - Santé (FRQS).

Position summary
The Proteomics and Molecular Analysis Platform, part of the Centre for Translational Biology at the RI-MUHC, is a specialized core facility supporting approximately 100 fundamental biomedical researchers, clinical investigators, and industrial clients. The platform provides a comprehensive range of services, from rapid biomarker profiling to deep proteome characterization.

The platform operates advanced instrumentation and automated workflows, including the Orbitrap Astral Zoom, Evosep ENO, and Beckman i5 liquid handler. These are supported by modern nDIA pipelines, AI-assisted analytics, and integrated sample processing infrastructure.

We are seeking a highly qualified Proteomics and Bioinformatics scientist to contribute to both the scientific direction and operational activities of the platform. The role combines, advanced bioinformatics, and hands-on expertise in LC-MS/MS-based proteomics workflows within a high-throughput core facility environment. The successful candidate will report to the Platform Manager and work closely with the Platform Director and broader team.

General Duties

Client Services and Scientific Leadership
• Lead client-facing activities including experimental design (including LC-MS/MS strategies), project planning, data analysis, interpretation, and reporting of results,
• Provide technical guidance and mentorship to investigators, trainees and collaborators,
• Contribute to the development and expansion of proteomics services within the platform,
• Participate in business development initiatives by supporting engagement with academic, clinical, and industry clients,
• Contribute to preparation of proposals, project scopes, and presentations,

Bioinformatics Infrastructure and Pipeline Development
• Design, develop, and maintain bioinformatics infrastructure supporting integrated workflows,
• Develop and maintain pipelines for DIA and DDA data using tools such as FragPipe, DIA-NN and the Monash Analyst Suite,
• Implement QA/QC procedures and data tracking systems for nDIA-based services,
• Evaluate and incorporate new computational and AI-based tools where appropriate,
LC-MS/MS and Proteomics Workflows
• Provide expertise in LC-MS/MS experimental design, acquisition strategies (DIA/DDA), and optimization of proteomics workflows,
• Collaborate with laboratory staff to optimize sample preparation, chromatography, and instrument performance for high-quality data acquisition,
• Contribute to method development and implementation of advanced LC-MS/MS approaches (, nDIA, high-throughput workflows, deep proteome profiling),
• Support troubleshooting of LC-MS/MS experiments and ensure data quality across projects,
• Maintain awareness of emerging technologies and best practices in mass spectrometry-based proteomics,

Research and Knowledge Dissemination
• Participate in scientific writing, including publications and grant applications,
• Contribute to training activities and user support,

Platform Operations
• Collaborate with laboratory staff to ensure alignment between sample processing and data analysis,
• Perform sample preparation tasks when required,
• Assist with coordination of platform activities including scheduling and project tracking,
• Contribute to continuous improvement of LC-MS/MS workflows, throughput, and data quality in alignment with platform growth objectives,
• Conduct other related tasks as assigned by the Platform Manager.

Website of the organization

Coup d'oeil video

Education / Experience

Education: Doctorate Degree
Field of Study: Proteomics, Bioinformatics, Computational Biology, or a related discipline

Experience: 5 years and more

Required Skills

• Advanced knowledge of oral and written French is required.
• An advanced knowledge of oral and written English is required, as the position requires regular and complex contact with patients, with researchers or international students who are exclusively proficient in English.

• 5+ years of relevant experience in proteomics, bioinformatics, and/or LC-MS/MS workflows (post-PhD or equivalent experience),
• Strong experience with proteomics data analysis, particularly DIA workflows,
• Proficiency in R and/or Python,
• Experience with tools such as FragPipe and DIA-NN,
• Familiarity with Thermo Orbitrap instrumentation,
• Strong hands-on experience with LC-MS/MS workflows,
• Working knowledge of Linux and Windows systems,
• Strong communication and organizational skills,
• Ability to work both independently and collaboratively,

• Additional assets:
o Experience with AI/ML approaches,
o Familiarity with clinical research environment,
o Experience with workflow tools such as Docker, Nextflow, or Snakemake,
o Previous experience in a core facility setting,
o Experience with automated sample preparation systems