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Associate Director, Protein Bioanalysis and Characterization

Prometheus Biosciences
San Diego, California
Start date
Jun 1, 2023

View more

Science/R&D, Chemistry, Laboratory
Required Education
Masters Degree/MBA
Position Type
Full time
Biotech Beach, Best Places to Work

Job Details




Associate Director, Protein Bioanalysis and Characterization - San Diego, CA


We’re a different kind of biotech company.  And we’re here to make a difference.


Prometheus Biosciences, Inc. (Nasdaq: RXDX), is a clinical-stage biotechnology company pioneering a precision medicine approach for the discovery, development, and commercialization of novel therapeutic and companion diagnostic products for the treatment of immune-mediated diseases. 


The Company’s precision medicine platform, Prometheus360™, combines proprietary machine learning-based analytical approaches with one of the world’s largest gastrointestinal bioinformatics databases to identify novel therapeutic targets and develop therapeutic candidates to engage those targets.  Headquartered in San Diego, Prometheus Biosciences, Inc. was named Best Places to Work by Biospace, San Diego Business Journal and is a Great Place to Work-Certified™ Company.


Prometheus Biosciences is looking for an expert in protein LCMS bioanalysis to lead projects supporting clinical biomarkers, R&D and CMC characterization. This position is expected to build an internal capability, develop methods, and transition/lead outsourced projects; determine the analytical strategy, translate project needs into assay solutions, be a mentor and may manage team members.  Also will apply sample preparation and enrichment methods including antibody-free approaches, protein, and peptide immunoaffinity in conjunction with LCMS-based detection using high resolution and triple quadrupole MS.  This position will work in project teams and interact closely with project leads, biologists, and protein engineers.


Key Duties and Responsibilities

  • Develop LCMS methods for quantitation and characterization of drug candidates and biomarkers from complex biological samples (e.g. blood, serum, tissues).  Utilize mass spectrometry to explore novel biomarker hypotheses, assist in optimization of existing workflows, and help to drive innovation.
  • Support CMC DS and DP characterization, including glycan profiling, disulfide and peptide mapping, post-translational modifications, and determination of intact mass.
  • As an experienced mentor, directly collaborate with others at all levels on projects and technology development.
  • Lead implementation and exploration of novel concepts and innovative workflows to expand the group’s biomarker bioanalytical capabilities.
  • Participate in all phases of mass spectrometry laboratory operations including technology evaluations, the development of sample preparation and separation methods, data analysis, interpretation, reporting and follow up discussions with the project teams on utilizing the data in appropriate decision making.
  • Act as key point of contact with external laboratories, including leading selection, qualification, and performance evaluation, including periodic visits to CRO laboratories conducting clinical biomarker assays.
  • Compose and review relevant portions of IND, IMPD, NDA/BLA/MAA, IB study protocols, SAPs and CSRs, or other regulated documents.
  • Collaborate closely with members of the project development teams, including members from non-clinical and clinical, bioanalytical and regulatory teams.
  • Liaise externally with key opinion leaders in industry and regulatory agencies, participate and present in scientific meetings.  Build relationships with KOLs, partners, and contract research organizations (CROs).


Education and Experience

  • PhD in Protein Biochemistry, Analytical Chemistry, or a related discipline with at least 12 years of relevant post-degree experience.
  • Experience in establishing an analytical lab, including instrument acquisition, hiring and training, assay development and implementation.
  • Expertise in development, characterization, qualification, and validation of biomarker assays based on quantitative protein mass spectrometry for drug development.
  • Experience and knowledge in operation of modern triple quadrupole, time-of-flight, and ion trap/orbitrap mass spectrometers and associated data analysis software systems.
  • Knowledge and application of complex sample preparation methodologies as applied to quantitative protein mass spectrometry workflows techniques including immuno-analytical techniques and tissue preparation/tissue bioanalysis.
  • Experience with antibody purification, developability, kinetics and biophysical characterization is a plus.

Skills and Abilities

  • Excellent verbal and written communication and strong presentation skills.
  • Proven ability to work effectively and collaboratively as a member of a multidisciplinary team.
  • Strong publication record in peer-reviewed journals a plus.

The anticipated base pay range for this position is $150,000 to $255,000. Individual pay is determined by job-related skills, experience, and relevant education or training. 


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Prometheus Biosciences is a biotech company pioneering a precision medicine approach for the discovery, development, and commercialization of novel therapeutic and companion diagnostic product candidates. While our initial focus was on IBD, we're now extending beyond gastrointestinal (GI) diseases to target other autoimmune diseases.

Prometheus360TM, our powerful precision medicine platform, combines proprietary technology with the world's most comprehensive collection of IBD patient data, to translate deep, complex data into precision therapeutic and diagnostic product candidates and continually identify new drug targets and unique disease biomarkers. We're headquartered in San Diego, CA.


Find Us
(858) 824-0895
3050 Science Park Road
San Diego
United States

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