Senior Scientist, Analytical Development & Quality Control

Protagonist Therapeutics; Newark (CA); On-site; USD 140,000 - 160,000; Full time

Benefits offered by this job

Health care benefits

401(k) Plan

Flexible vacation policy

Life Insurance

Short/Long-term disability

Lunch and snacks

Job summary

Protagonist Therapeutics is seeking a talented Senior Scientist to join the Analytical Development & Quality Control (ADQC) group in Newark, CA. The role drives analytical development strategies for small molecules and peptides, including method development, validation, transfer, and stability programs for DS and DP.

You will lead internal activities and manage CDMO partnerships to achieve program objectives.

Qualifications

• PhD or MS in Analytical Chemistry or a relevant scientific discipline with 5+ years in CMC development.
• Experience developing analytical methods for peptides or complex drug substances.
• Strong experience managing analytical development and QC functions at CDMOs.
• Proven ability to lead projects, communicate with stakeholders, and meet timelines.

Responsibilities

• Develop, optimize, and validate methods for release, stability, and characterization of DS/DP.
• Lead impurity identification, degradant analysis, method transfer, and lifecycle management.
• Establish robust analytical control strategies for clinical and regulatory needs.
• Triage OOS/OOT events, deviations, CAPA, and change control.
• Manage stability and reference standards programs; liaise with CDMOs.
• Prepare regulatory filings sections and support Module 3 inputs.
• Drive continuous improvement in processes and CDMO management.
• Represent ADQC in cross-functional team meetings.

Skills

UHPLC method development

Analytical method validation

CDMO management

Regulatory awareness

Cross-functional collaboration

Team leadership

Education

PhD or MS in Analytical Chemistry

Tools

UHPLC

MS

cGMP/GLP

Job description

About Us

Protagonist Therapeutics is a discovery-through-late-stage development biopharmaceutical company with a proprietary technology platform that enables de novo discovery of peptide therapeutics. Two novel peptides derived from Protagonist's proprietary discovery platform are at or near commercialization. ICOTYDE™ (icotrokinra), licensed to Johnson & Johnson company Janssen Biotech, Inc., is the first and only targeted oral peptide that precisely blocks the Interleukin-23 receptor. ICOTYDE was launched in the U.S. in March 2026, is approved for the treatment of moderate-to-severe plaque psoriasis in adults and pediatric patients 12 years of age or older and is in Phase 3 development for psoriatic arthritis, ulcerative colitis and Crohn's disease. ICOTYDE was jointly discovered by Protagonist and Johnson & Johnson scientists, with Protagonist having primary responsibility for the development of ICOTYDE through Phase 1, and Johnson & Johnson assuming responsibility for further development and commercialization. Protagonist also discovered and led development through Phase 3 of rusfertide, a first-in-class hepcidin mimetic peptide licensed to Takeda Pharmaceuticals. An NDA for rusfertide for the treatment of polycythemia vera is under priority review with the FDA. The Company also has a number of clinical and preclinical programs addressing clinically and commercially validated targets, including an oral IL-17 antagonist peptide, obesity dual and triple agonists, an oral hepcidin functional mimetic, and the recently announced IL-4 and amylin programs.

More information on Protagonist, its pipeline drug candidates, and clinical studies can be found on the Company's website at https://www.protagonist-inc.com.

Position Summary

Protagonist Therapeutics is seeking a talented and highly motivated Senior Scientist to join the Analytical Development & Quality Control (ADQC) group. The successful candidate will help drive analytical development strategy for small-molecule and peptide candidates from early development through late-stage programs, including analytical method development, validation, transfer, stability programs, phase-appropriate specifications, and analytical control strategies for drug substance (DS) and drug product (DP). This role includes leading internal analytical activities, managing external CDMO partners, and collaborating closely with Drug Substance, Drug Product, Supply Chain, Quality Assurance, Regulatory, Nonclinical, and Clinical teams to achieve program objectives. This position reports to the Senior Director of ADQC.

We are committed to a thriving in-office culture. This role requires being on-site at our office in Newark, CA 4 days a week.

Responsibilities

• Develop, optimize, and validate analytical methods for release, stability, and characterization testing of DS and DP.
• Lead impurity identification, degradant analysis, comparability assessments, method transfer, and analytical method lifecycle management.
• Establish phase-appropriate, scientifically robust analytical control strategies, including characterization plans and specification setting, to support clinical and regulatory requirements and enable accelerated development timelines.
• Troubleshoot analytical issues and support investigations, including OOS/OOT results, deviations, root-cause analysis, CAPA recommendations, and change-control activities, as applicable.
• Manage stability and reference standard programs for assigned projects.
• Communicate effectively with stakeholders and manage analytical development and QC testing activities at CDMOs.
• Review CDMO data for release testing, stability testing, and DS/DP characterization to ensure scientific rigor, data integrity, and compliance.
• Author analytical sections for regulatory filings, including INDs, IMPDs, and NDAs, and provide input to relevant Module 3 sections.
• Participate in continuous improvement initiatives, including process and workflow improvements, CDMO management practices, and SOP development or revision in collaboration with Quality Assurance.
• Represent ADQC in cross-functional team meetings.

Required Skills & Qualifications

• PhD or MS in Analytical Chemistry or a relevant scientific discipline, with 5+ years of experience supporting early- and late-stage CMC development.
• Hands-on expertise in UHPLC method development using a range of detection technologies, including UV, PDA, MALS, CAD, conductivity, fluorescence, and advanced MS for identification and structural characterization.
• Extensive experience developing analytical methods for synthetic peptides or similarly complex drug substance molecules, such as ADCs, PEGylated proteins, or monoclonal antibodies, is highly preferred.
• Demonstrated ability to solve complex scientific and business challenges.
• Extensive experience communicating with and managing analytical development and QC functions at CDMOs.
• Strong knowledge of cGMP/GLP compliance, pharmaceutical quality systems, and regulatory requirements for drug development.
• Excellent written and verbal communication skills, with the ability to effectively represent analytical development plans to CDMOs, internal project teams, CMC teams, and senior management.
• Ability to manage priorities and maintain timelines in a fast-paced environment while balancing speed, quality, and risk.
• Strong project management, communication, leadership, and cross-functional collaboration skills.
• Experience in small- to mid-size innovator companies is desired.
• Ability to travel domestically and internationally, as needed.

Pay Range

The base pay range for this position at commencement of employment is expected to be between $140,000 and $160,000/year; however, base pay offered may vary depending on multiple individualized factors, including market location, job-related knowledge, skills, and experience.

Benefits

A top priority for Protagonist Therapeutics, Inc. is to provide a robust and comprehensive health and wellness program for our employees and their families. We offer a variety of high-quality coverage and benefit options.

• Health Care benefits. Protagonist covers 100% of the premium cost for medical, dental, and vision coverage for all full-time employees and their dependents.
• Flexible Spending Accounts – Healthcare FSA, Dependent Care FSA, Commuter Benefits
• 401(k) Plan
• Flexible Vacation Policy
• Life Insurance (Basic, Voluntary & AD&D)
• Short Term & Long Term Disability
• Company paid lunch and snacks