Scientist - Proteomics

Dana-Farber Cancer Institute; Boston, Northern (MA, KY); Hybrid; USD 80,000 - 96,000; Full time

Job summary

Dana-Farber Cancer Institute in Boston is seeking a Scientist I / Research Scientist to join the TPD Core. The role uses mass spectrometry to study proteome-wide responses to perturbations and contribute to projects on targeted protein degradation with emphasis on automation and workflow development.

You will lead experiments (TMT, DIA, DDA), maintain instruments, and collaborate across teams to advance cancer biology research while upholding data integrity and safety standards.

Qualifications

• Ph.D. in biochemistry, analytical chemistry, bioengineering or related field.
• Strong expertise in mass spectrometry-based proteomics and data analysis.
• Hands-on experience operating Thermo and/or Bruker mass spectrometers.
• Experience with laboratory automation, robotics, or pipeline development.
• Proficiency with quantitative proteomics and enrichment techniques.
• Familiarity with data analysis software and scripting (DIA-NN, Proteome Discoverer, R, Python).
• Excellent organizational, troubleshooting, and communication skills.
• Proven ability to work collaboratively across interdisciplinary teams.

Responsibilities

• Lead the design and execution of proteomics experiments (eg, TMT, DIA, DDA).
• Develop and implement automated workflows for sample prep, instrument scheduling, data acquisition, and analysis.
• Manage and maintain mass spectrometry instrumentation and preventive maintenance.
• Integrate laboratory robotics and liquid handling into proteomics pipelines.
• Develop, optimize, and troubleshoot sample prep workflows including whole cell proteomics and interactome analyses.
• Analyze data using advanced pipelines and support biological interpretation.
• Train and mentor junior staff and contribute to continuous improvement.
• Ensure compliance with lab safety, QC standards, and data integrity policies.
• Communicate with purchasing and negotiate with vendors.

Skills

Mass spectrometry

Proteomics

Data analysis

Laboratory automation

Instrument operation

Scripting (R/Python)

Education

Ph.D in biochemistry / analytical chemistry / bioengineering or related field

Tools

Thermo mass spectrometers

Bruker mass spectrometers

Job description

The Targeted Protein Degradation (TPD) Proteomics Core in the Fischer Lab at Dana-Farber Cancer Institute supports Cancer Biology researchers by using mass spectrometry-based proteomics to address important scientific questions. The core applies quantitative chemoproteomics and interaction proteomics to uncover drug targets and continues to broaden its capabilities to serve a growing research community. Its instrumentation includes advanced platforms such as the timsTOF HT, timsTOF Ultra2, and Orbitrap Eclipse Tribrid mass spectrometers.

We are seeking a driven and collaborative Scientist I / Research Scientist to join the TPD Core team. In this role, the scientist will use mass spectrometry technologies to study proteome-wide cellular responses to external perturbations and contribute to projects centered on targeted protein degradation as an emerging therapeutic strategy, with particular interest in individuals who bring expertise in laboratory automation, instrument operations, systems oversight, and proteomics workflow development.

Located in Boston and the surrounding communities, Dana-Farber Cancer Institute is a leader in life changing breakthroughs in cancer research and patient care. We are united in our mission of conquering cancer, HIV/AIDS, and related diseases. We strive to create an inclusive, diverse, and equitable environment where we provide compassionate and comprehensive care to patients of all backgrounds, and design programs to promote public health particularly among high-risk and underserved populations. We conduct groundbreaking research that advances treatment, we educate tomorrow's physician/researchers, and we work with amazing partners, including other Harvard Medical School-affiliated hospitals.

• Lead the design and execution of proteomics experiments (eg, TMT, DIA, DDA) in collaboration with internal and external investigators.
• Develop and implement automated workflows for sample preparation, instrument scheduling, data acquisition, and analysis across multiple platforms.
• Manage and maintain mass spectrometry instrumentation, including calibration, performance monitoring, and preventive maintenance to ensure high-throughput reliability.
• Integrate laboratory robotics and liquid handling systems into proteomics sample preparation pipelines to enhance throughput and reproducibility.
• Develop, optimize, and troubleshoot sample preparation workflows including whole cell proteomics, interactome analysis, and various enrichment protocols.
• Analyze data using advanced pipelines (eg, DIA-NN, spectronaut, proteome discoverer) and support biological interpretation.
• Train and mentor junior staff and contribute to a culture of continuous improvement.
• Ensure compliance with lab safety, QC standards, and data integrity policies.
• Communicates with purchasing and may be responsible for negotiating with vendors.

QUALIFICATIONS

• Ph.D in biochemistry, analytical chemistry, bioengineering or related field.
• Strong expertise in mass spectrometry-based proteomics and data analysis.
• Hands on experience operating Thermo and/or Bruker mass spectrometers is required.
• Demonstrated experience with laboratory automation, robotics, or pipeline development (e.g., Hamilton, Opentrons, or custom scripting for workflow automation).
• Proficiency with quantitative proteomics (label-free, TMT, DIA) and enrichment techniques.
• Familiarity with data analysis software and scripting (DIA-NN, Proteome Discoverer, R, Python).
• Excellent organizational, troubleshooting, and communication skills.
• Proven ability to work collaboratively across interdisciplinary teams and manage multiple projects simultaneously.

License/Certification/Registration Required: None

Supervisory Responsibilities: No

Patient Contact: None

At Dana-Farber Cancer Institute, we work every day to create an innovative, caring, and inclusive environment where every patient, family, and staff member feels they belong. As relentless as we are in our mission to reduce the burden of cancer for all, we are committed to having faculty and staff who offer multifaceted experiences. Cancer knows no boundaries and when it comes to hiring the most dedicated and compassionate professionals, neither do we.

Dana-Farber Cancer Institute is an equal opportunity employer and affirms the right of every qualified applicant to receive consideration for employment without regard to race, color, religion, sex, gender identity or expression, national origin, sexual orientation, genetic information, disability, age, ancestry, military service, protected veteran status, or other characteristics protected by law.

EEO Poster

Pay Transparency Statement

The hiring range is based on market pay structures, with individual salaries determined by factors such as business needs, market conditions, internal equity, and based on the candidate’s relevant experience, skills and qualifications.

For union positions, the pay range is determined by the Collective Bargaining Agreement (CBA).

$80,000.00 - $95,900.00