Senior Scientist, High-Throughput Mass Spectrometry (Automation)

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Job Description

At Takeda, we are a forward-looking, world-class R&D organization that unlocks innovation and delivers transformative therapies to patients. By focusing R&D efforts on three therapeutic areas and other targeted investments, we push the boundaries of what is possible to bring life-changing therapies to patients worldwide.

Objective / Purpose:

The Senior Scientist will play a pivotal role in Takeda’s “Lab of the Future” initiative, driving the design, miniaturization, and execution of robust bioanalytical assays on fully automated, integrated platforms. Leveraging advanced automation systems and statistical analysis, this individual will ensure high-throughput, reproducible, and high-quality data generation to support iterative AI-integrated Design–Make–Test–Analyze (DMTA) cycles for both small- and large-molecule discovery. The Senior Scientist will partner closely with DMPK, medicinal chemistry, data sciences, and automation engineering to translate complex bioanalytical data into actionable insights that accelerate portfolio progression and enable data-driven decision-making. This role contributes to critical function delivery as follows:

• Accelerates Discovery through Automation and AI-Integrated DMTA: Designs and executes bioanalytical assays in 384- and 1,536-well formats on fully automated, robotic platforms with integrated workflows, enabling rapid, high-throughput testing and iterative optimization.
• Ensures Data Quality and Scientific Rigor: Applies statistical methodologies to evaluate assay performance (e.g., Z’ factor, variability metrics, curve-fit confidence) and maintains reproducibility and reliability of decision-enabling datasets.
• Drives Cross-Functional Impact: Partners with DMPK, medicinal chemistry, and data science teams to interpret bioanalytical data in the context of SAR, disease biology, and mechanism-of-action, informing compound progression and portfolio decisions.

Accountabilities:

Advance Automated Bioanalytical Lead Profiling

• Design, develop, optimize, and validate bioanalytical assays supporting hit identification, hit-to-lead, and lead optimization programs for small and large molecules.
• Drive assay miniaturization to 384- and 1,536-well formats, ensuring robustness, reproducibility, and biological relevance.
• Implement statistically rigorous assay performance standards (e.g., Z’ factor, signal-to-background, CV, curve-fit quality metrics) to ensure data integrity and confidence in decision-making.

Enable Efficient DMTA Cycles

• Execute DMTA lead profiling assays, ensuring reliable, timely delivery of high-quality MS data across small- and large-molecule modalities.
• Adapt and translate bioanalytical assays to high-throughput MS platforms (e.g., Acoustic MS, RapidFire MS, MALD-MS or other).
• Continuously improve workflows to shorten cycle times and increase throughput while maintaining quality.

Operate Within Fully Integrated, Automated Systems

• Develop and execute assays on fully automated robotic platforms, including liquid handling systems, acoustic dispensing, and multimode detection technologies.
• Partner with automation engineers to design scalable, modular workflows aligned with Lab of the Future principles.
• Contribute to seamless integration of instrumentation with LIMS/ELN systems, scheduling software, and digital data pipelines to enable end-to-end automation.

Ensure Data Excellence & AI-Readiness

• Apply advanced statistical analysis and visualization tools to assess assay robustness, variability, and data quality.
• Ensure datasets are standardized, curated, and appropriately annotated to support AI/ML-driven analytics and cross-program insights.
• Contribute to data governance practices that promote longitudinal learning across Takeda’s discovery portfolio.

Collaborate Across Takeda

• Partner closely with DMPK, medicinal chemistry, data sciences, and translational sciences to advance program objectives.
• Communicate findings clearly in cross-functional forums and contribute to scientific discussions that shape portfolio decisions.
• Uphold Takeda’s values of Integrity, Fairness, Honesty, and Perseverance in all scientific and operational activities.

Education & Competencies (Technical and Behavioral):

• Expected: Ph.D. in Analytical Chemistry, Biochemistry, Pharmaceutical Sciences, or related discipline with at least 2+ years of industry experience; OR M.S. with 8+ years; OR B.S. with 10+ years of relevant experience with pharmaceutical or biotech R&D.
• Deep hands-on expertise in high-throughput MS (e.g., acoustic MS, RapidFire MS, MALDI-MS or other platforms), with a track record of developing and running high-throughput MS assays.
• Proven expertience working with DMTA or screening workflows.
• Working knowledge of integrated HTS automation systems and robotic platforms, including programming, configuring, and troubleshooting liquid handlers (e.g., Echo, Hamilton, Beckman, Agilent).
• Hands-on familiarity with scheduling software, LIMS/ELN, and data pipeline tools commonly used in automated labs.
• Proficiency with MS data analysis tools and software; experience with scripting or data handling (e.g., Python, R, Spotfire) is a plus.
• Demonstrated ability to work independently and collaboratively in a highly matrixed, cross-functional environment while managing multiple priorities and contribute to mentoring or guiding junior scientific staff.

Proven track record of:

• Developing and validating bioanalytical assays for drug discovery.
• Adapting bioanalytical assays to high-throughput MS platforms; including miniaturization, and automation-friendly assay design.
• Experience in high-content, high-throughput environments, including design-of-experiments (DoE) approaches for optimization.
• Familiarity with LIMS/ELN systems and data pipeline tools.
• Running assays on fully automated, robotic platforms in high-throughput environments.
• Successful miniaturization of assays to at least 384-well and preferably 1,536-well plate formats.

ADDITIONAL INFORMATION

• The position will be based in Cambridge, MA. 

Takeda Compensation and Benefits Summary

We understand compensation is an important factor as you consider the next step in your career. We are committed to equitable pay for all employees, and we strive to be more transparent with our pay practices.

For Location:

Boston, MA

U.S. Base Salary Range:

$137,000.00 - $215,270.00

The estimated salary range reflects an anticipated range for this position. The actual base salary offered may depend on a variety of factors, including the qualifications of the individual applicant for the position, years of relevant experience, specific and unique skills, level of education attained, certifications or other professional licenses held, and the location in which the applicant lives and/or from which they will be performing the job. The actual base salary offered will be in accordance with state or local minimum wage requirements for the job location. 

U.S. based employees may be eligible for short-term and/ or long-term incentives. U.S. based employees may be eligible to participate in medical, dental, vision insurance, a 401(k) plan and company match, short-term and long-term disability coverage, basic life insurance, a tuition reimbursement program, paid volunteer time off, company holidays, and well-being benefits, among others. U.S. based employees are also eligible to receive, per calendar year, up to 80 hours of sick time, and new hires are eligible to accrue up to 120 hours of paid vacation. 

EEO Statement

Takeda is proud in its commitment to creating a diverse workforce and providing equal employment opportunities to all employees and applicants for employment without regard to race, color, religion, sex, sexual orientation, gender identity, gender expression, parental status, national origin, age, disability, citizenship status, genetic information or characteristics, marital status, status as a Vietnam era veteran, special disabled veteran, or other protected veteran in accordance with applicable federal, state and local laws, and any other characteristic protected by law.

Locations

Boston, MA

Worker Type

Employee

Worker Sub-Type

Regular

Time Type

Job Exempt

Yes

It is unlawful in Massachusetts to require or administer a lie detector test as a condition of employment or continued employment. An employer who violates this law shall be subject to criminal penalties and civil liability.