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Scientist II - Proteomics

San Diego, California


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Scientist II - Proteomics

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Job ID R0030700 Date posted 03/02/2021 Location San Diego, California

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Job Description

Are you looking for a patient-focused, innovation-driven company that will inspire you and empower you to shine?  Join us as a Scientist in Scientist II Proteomics at our  San Diego Research Site.

At Takeda, we are transforming the pharmaceutical industry through our R&D-driven market leadership and being a values-led company.  To do this, we empower our people to realize their potential through life-changing work. Certified as a Global Top Employer, we offer stimulating careers, encourage innovation, and strive for excellence in everything we do.   We foster an inclusive, collaborative workplace, in which our global teams are united by an unwavering commitment to deliver Better Health and a Brighter Future to people around the world.

Here, you will be a vital contributor to our inspiring, bold mission.  As a Scientist in Proteomics, you will be empowered to serve on project teams.


Contributes to design, development and execution of research assignments, potentially contributing to multiple projects

SCOPE Takeda’s Drug Discovery Sciences (DDS) team is seeking a collaborative, creative and talented mass spectrometrist to join our biophysics group. DDS is focused on delivering transformative therapies to patients by developing new technologies in emergent areas of drug discovery such as targeted protein degradation and small molecule RNA modulators.

Senior Scientist-Mass Spectrometry will design, develop, and implement proteomics and chemo-proteomics strategies to accelerate drug discovery programs in the areas of Oncology, Neurosciences, Rare and Gastrointestinal diseases.  Senior Scientist-Mass Spectrometry will also stablish and lead external collaborators with private and academic institutions to access new technologies and develop novel approaches to accelerate Takeda’s drug discovery efforts.


  • Design and perform quantitative proteomics, isobaric labeling (TMT, iTRAQ), label-free quantification and peptide fragmentation experiments
  • Stablish engagement (pSILAC) and label-free proteome profiling (DART, SPROX) assays
  • Lead bottom-up mass spectrometry-based studies for in cell and in-vitro quantitative proteomics
  • Develop and implement approaches for small molecule target identification, engagement and validation (site-selective protein modification, photo affinity cross-linking, activity-based protein profiling (ABPP).


Technical/Functional (Line) Expertise

  • Expertise in quantitative proteomics techniques, isobaric labeling methods (TMT, iTRAQ), label-free quantification approaches and peptide fragmentation methods
  • Experience in target engagement methods (pSILAC) and label-free proteome profiling (DART, SPROX)
  • Experience in bottom-up mass spectrometry-based applications for in cell and in-vitro quantitative proteomics
  • Biologics characterization using mass spectrometric methods
  • Experience with E3 ubiquitin ligases, molecular degrader technologies is a plus
  • Proficiency in small molecule target identification, engagement and validation.
  • Expertise in biorthogonal chemistry, site-selective protein modification, photo affinity cross-linking, activity-based protein profiling (ABPP) is a plus.
  • Experience and knowledge in the operation and maintenance of different types of mass spectrometers including Q Exactive and Orbitrap Eclipse Tribrid
  • Experience with quantitative proteomics data analysis, including Proteome Discoverer, IP2, MaxQuant, or equivalent analysis platforms is required. 
  • Experience in the operation, minor maintenance, troubleshooting, and calibration of laboratory equipment required
  • Programming expertise is a plus.


  • Identifies, plans and executes novel scientific projects and may manage the work of others a direct or matrixed structure

Decision-making and Autonomy

  • Independently manages workload and expectations
  • Scientifically independent
  • May influence decision making within the department


  • Conducts scientific presentations to internal audiences


  • Receives high level instructions on all work, determines methods on new assignments, works closely with manager, may manage junior staff


  • PhD degree in a scientific discipline with 2+ years experience , or
  • MS with 8+ years experience, or
  • BS with 10+ years experience

This job posting excludes CO applicants


  • 401(k) with company match and Annual Retirement Contribution Plan
  • Tuition reimbursement
  • Company match of charitable contributions
  • Health & Wellness programs including onsite flu shots and health screenings
  • Generous time off for vacation and the option to purchase additional vacation days
  • Community Outreach Programs

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San Diego, CA

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Full time

Job ID R0030700
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