Associate Director, High-Throughput Mass Spectrometry

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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:

Takeda is building the “lab of the future” to power faster, smarter decision-making across our discovery and development portfolio. As an Associate Director High-Throughput Mass Spectrometry (Acoustic MS) within the Lead Profiling / DMTA team, you will be a key technical and strategic contributor enabling high-throughput, high-quality data generation for DMTA (Design–Make–Test–Analyze) cycles.

You will be responsible for developing, implementing, and running high-throughput mass spectrometry workflows to support lead profiling and ADME assays. This role will report directly to the Head of Lab Automation and Transformation and will be central to shaping and scaling Takeda’s next-generation, automated screening and profiling capabilities.

Accountabilities:

• High-Throughput Mass Spectrometry & Acoustic MS
  • Lead the design, development, and optimization of high-throughput MS workflows, with a primary focus on acoustic MS platforms for small-molecule and biotherapeutic lead profiling.
  • Own the end-to-end lifecycle of acoustic MS methods—from feasibility and method development through validation, troubleshooting, and routine deployment.
  • Drive continuous performance improvements in sensitivity, robustness, throughput, and cost-per-sample across MS workflows.
• DMTA Lead Profiling & ADME Support
  • Execute and oversee DMTA lead profiling assays, ensuring reliable, timely delivery of high-quality MS data for project teams.
  • Adapt and translate ADME assays (e.g., solubility, permeability, metabolic stability, protein binding) to high throughput MS formats, leveraging miniaturization and automation to increase throughput and reduce cycle time.
  • Partner with DMPK, medicinal chemistry, biology, and data science functions to align assay design and data outputs with decision-making needs across discovery programs.
• Lab Automation & Lab of the Future
  • Collaborate closely with the Lab Automation and Transformation organization to integrate MS platforms into end-to-end automated workflows (sample preparation, plate handling, liquid handling, scheduling, data capture).
  • Provide scientific and technical input into the design and selection of new instruments, automation hardware, and software to support the lab of the future vision.
  • Contribute to digitalization efforts by helping define data standards, metadata capture, and connectivity between instruments, LIMS/ELNs, and analytics platforms.
• Operational Excellence & Quality
  • Establish and maintain robust QC procedures, SOPs, and best practices for high-throughput MS operations, including system suitability and performance monitoring.
  • Drive root-cause investigations and implement corrective actions when assay performance drifts or system issues arise.
  • Ensure data integrity, reproducibility, and compliance with Takeda quality and safety standards.
• Collaboration, Influence & Leadership
  • Act as the subject matter expert (SME) for high-throughput and acoustic MS within the lead profiling and automation communities at Takeda.
  • Provide training, mentorship, and technical guidance to scientists and associates on MS methods, data interpretation, and troubleshooting.
  • Communicate clearly with interdisciplinary stakeholders, presenting complex technical topics in an accessible way to both scientific and non-scientific audiences.

Education & Experience:

• Expected: Ph.D. in Analytical Chemistry, Biochemistry, Pharmaceutical Sciences, or related field, 6+ years of relevant industry/postdoctoral experience is expected; OR M.S. with 12 years of relevant experience; OR B.S. with 14 years of relevant experience in pharmaceutical / biotech R&D.
• Deep hands-on expertise in mass spectrometry, with a track record of developing and running high-throughput MS assays.
• Critical: Demonstrated, hands-on experience with acoustic MS platforms (e.g., method development, optimization, troubleshooting, and routine operation).
• Strong experience in quantitative bioanalytical methods for small molecules and/or biotherapeutics (e.g., direct MS, LC–MS, or acoustic MS-based quantitation).
• Proven experience working with DMTA or screening workflows, preferably in lead profiling or DMPK/ADME support.
• Proficiency with MS data analysis tools and software; experience with scripting or data handling (e.g., Python, R, Spotfire) is a plus.

Proven track record of:

• Adapting ADME assays to acoustic MS, including miniaturization, plate-based workflows, and automation-friendly assay design.
• Experience integrating MS instruments with automated sample preparation and plate handling systems (liquid handlers, robotic arms, plate stackers, schedulers).
• Experience in high-content, high-throughput environments, including design-of-experiment (DoE) approaches for optimization.
• Familiarity with LIMS/ELN systems and data pipeline tools, including integration of instrument outputs into central data lakes or analytics platforms.
• Background in drug discovery lead optimization and understanding of how ADME and profiling data inform structure–activity relationships and project decisions.

ADDITIONAL INFORMATION

• The position will be based in Cambridge, MA.This position is currently classified as “hybrid” by Takeda’s Hybrid and Remote Work policy

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:

$153,600.00 - $241,340.00

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

Full time

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.