Sr. Scientist, Analytical Development & Quality Control

BioPhase; San Diego (CA); On-site; USD 120,000 - 170,000; Full time

Job summary

BioPhase is seeking a Senior Scientist for the Analytical Development & Quality Control group. You will apply analytical chemistry to oligonucleotide therapeutics using QTOF-MS, LC-MS, HPLC, GC, and MALS in a GMP setting.

Independent, detail-oriented, and collaborative, you will advance method development, reference standard characterization, and regulatory submissions. Responsibilities include method validation, impurity profiling, investigation of OOS/OOT cases, and contributing to IND/NDA/MAA

Qualifications

• Ph.D. in Analytical Chemistry or related field with 2+ years in industry; or M.S. with 8+ years.
• Hands-on analytical development for oligonucleotide therapeutics (ASOs, siRNA or related modalities).
• Advanced QTOF MS proficiency for oligonucleotide characterization and impurity profiling.
• Expertise in ion-pair reversed-phase LC-MS for purity and impurity profiling.
• GMP laboratory experience and knowledge of ICH guidelines.

Responsibilities

• Develop and validate analytical methods for oligonucleotide drug substances and starting materials.
• Characterize reference standards using UV, MS, NMR, and hyphenated LC techniques.
• Conduct OOS and OOT investigations with root-cause analysis and CAPA development.
• Author analytical method validation packages and contribute to CMC sections of regulatory filings.
• Present findings at internal meetings and cross-functional teams.

Skills

QTOF MS

LC-MS

HPLC

GC

MALS

Oligonucleotide analytics

CMC submissions

Education

PhD in Analytical Chemistry

MS in Analytical Chemistry

Tools

Empower

MassLynx

Job description

We are seeking an experienced and motivated Senior Scientist to join our Analytical Development & Quality Control group. This individual will bring deep expertise in analytical chemistry applied to oligonucleotide therapeutics, with hands-on proficiency across a suite of advanced instrumentation including QTOF-MS, LC-MS, HPLC, and GC. The successful candidate will play a key role in developing and validating analytical methods for oligonucleotide drug substances and starting materials, characterizing reference standards, conducting analytical investigations, and contributing to CMC regulatory submissions — all within a GMP environment. This role requires a high degree of scientific independence, strong attention to detail, and the ability to thrive in a fast-paced, cross-functional setting.

Key Responsibilities

• Develop and validate analytical methods for oligonucleotide drug substances, starting materials, and related impurities using ion-pair reversed-phase HPLC, LC-MS, QTOF-MS, GC, and MALS.
• Apply high-resolution QTOF mass spectrometry for accurate mass determination, sequence confirmation, and detailed impurity profiling of phosphorothioate oligonucleotides and related analogs.
• Utilize MALS (Multi-Angle Light Scattering) for molecular weight determination and aggregation characterization of oligonucleotide drug substances.
• Characterize new reference standards using a broad range of orthogonal analytical techniques including UV, MS, NMR, and hyphenated LC techniques.
• Conduct routine and non-routine analysis of raw materials and starting material samples; review data for compliance to established specifications.
• Design and execute analytical investigations, including out-of-specification (OOS) and out-of-trend (OOT) investigations, with thorough root cause analysis and CAPA development.
• Author scientific reports, analytical method validation packages, and contribute to CMC sections of IND, NDA, and MAA regulatory filings.
• Write and revise SOPs, analytical methods, equipment procedures, and material specifications in accordance with GMP requirements.
• Develop stability-indicating methods and contribute to stability programs for oligonucleotide drug substances and drug products.
• Present scientific findings at internal project meetings and cross-functional team discussions; contribute to external publications and conference presentations as appropriate.
• Serve as an analytical subject matter expert on cross-functional teams spanning process development, manufacturing, and regulatory affairs.

Requirements

• Ph.D. in Analytical Chemistry, Pharmaceutical Sciences, or a closely related discipline with 2+ years of relevant industry; or an M.S. with 8+ years of industry experience.
• Required: demonstrated hands-on experience in analytical development for oligonucleotide therapeutics (ASOs, siRNA, or related modalities). Candidates with oligonucleotide experience will be prioritized.
• Advanced proficiency with QTOF mass spectrometry for oligonucleotide characterization, impurity identification, and accurate mass analysis.
• Expertise in ion-pair reversed-phase LC-MS for oligonucleotide purity, assay, and impurity profiling, including method development and validation.
• Skilled in HPLC and GC method development and validation; familiarity with multiple detection modes (UV, fluorescence, CAD, MS).
• Thorough understanding of ICH guidelines (Q1, Q2, Q6) and FDA method validation requirements, including phase-appropriate strategies.
• Practical knowledge of GMP requirements; hands-on GMP laboratory experience strongly preferred.
• Experience authoring CMC sections of regulatory submissions (INDs, NDAs, or equivalent) is highly desirable.
• Strong problem-solving skills with ability to manage multiple priorities and meet aggressive timelines across concurrent projects.
• Excellent written and verbal communication skills; ability to present complex scientific data clearly to diverse audiences.
• Ability to work both independently and collaboratively within a matrix environment.

Preferred Qualifications

• Experience with 2D-LC or multidimensional chromatographic separations for complex oligonucleotide impurity profiling.
• Familiarity with accelerated stability assessment programs (ASAP) for oligonucleotide therapeutics.
• Knowledge of oligonucleotide chemical modifications including phosphorothioate backbones, 2'-modifications, and GalNAc conjugates.
• Experience with Empower, MassLynx, or equivalent chromatography data systems.
• Publication record or conference presentations in oligonucleotide analytics or related fields.