Sr. Scientist, Analytical Development & Quality Control

BioPhase; San Diego (CA); On-site; USD 140,000 - 190,000; Full time

Job summary

BioPhase is seeking a Senior Scientist to join the Analytical Development & Quality Control group. The role emphasizes analytical chemistry for oligonucleotide therapeutics, with hands-on expertise across QTOF-MS, LC-MS, HPLC, and GC in a GMP setting.

You will develop and validate methods for drug substances and starting materials, characterize reference standards, and contribute to regulatory submissions while working in a fast-paced, cross-functional environment.

Qualifications

• Ph.D. in Analytical Chemistry, Pharmaceutical Sciences, or related field with 2+ years industry, or an M.S. with 8+ years.
• Hands-on analytical development for oligonucleotide therapeutics (ASOs, siRNA).
• Experience with QTOF mass spectrometry for oligonucleotide characterization and impurity profiling.
• Expertise in ion-pair reversed-phase LC-MS for oligonucleotide purity and impurities.

Responsibilities

• Develop and validate analytical methods for oligonucleotide drug substances, starting materials, and related impurities.
• Apply high-resolution QTOF mass spectrometry for accurate mass determination, sequence confirmation, and impurity profiling.
• Utilize MALS for molecular weight determination and aggregation characterization.
• Characterize reference standards using UV, MS, NMR, and hyphenated LC techniques.
• Conduct routine and non-routine analysis of raw materials and starting materials; review data for compliance.
• Design and execute analytical investigations including OOS and OOT with root cause analysis and CAPA.
• Author scientific reports, method validation packages, and contribute to CMC sections of regulatory filings.
• Write and revise SOPs, methods, and GMP-compliant procedures.
• Develop stability-indicating methods and contribute to stability programs.
• Present findings at internal meetings; contribute to publications and conference presentations.
• Serve as analytical SME on cross-functional teams spanning process development, manufacturing, and regulatory affairs.

Skills

Analytical development

Problem solving

Written and verbal communication

Cross-functional collaboration

Education

Ph.D. in Analytical Chemistry or related field

M.S. in Analytical Chemistry or related field

Tools

QTOF-MS

LC-MS

HPLC

GC

MALS

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.