Senior Associate Scientist - Proteogenomics & Immunopeptidomics

Regeneron Pharmaceuticals • Tarrytown, GA

3d • $81,900 - $133,700

About The Position

Regeneron is seeking a Senior Associate Scientist to join a translational proteomics group discovering and validating novel cell-surface and HLA-presented antigens for therapeutic antibody, bispecific, and cell-therapy programs. The role works at the intersection of proteogenomics and immunopeptidomics, generating high-sensitivity LC-MS/MS data and helping translate peptide-level evidence into validated target candidates for discovery teams.

This is a hands-on laboratory position intended for someone who can develop expertise in specialized proteogenomics and immunopeptidomics methods through structured, direct training from experienced scientists. The position emphasizes strong laboratory fundamentals, careful bench work, and willingness to learn mass spectrometry. A master's degree is a good fit, and strong candidates with a bachelor's degree and relevant laboratory experience are welcome. Technical independence and career progression are expected to grow with experience.

The group combines laboratory and data-science approaches. Coding in Python or R and familiarity with machine learning or reproducible analysis workflows are not required; there is an opportunity to learn these skills with support, while laboratory work remains the core of the role. First-year training includes operation, calibration, routine maintenance, and first-line troubleshooting of Thermo Orbitrap and Bruker timsTOF mass spectrometers; nanoflow liquid chromatography; HLA class I and II immunoprecipitation; database searching and proteomics result interpretation with false-discovery control; and targeted PRM/MRM assays using stable isotope-labeled peptide standards.

The successful candidate will collaborate with colleagues in proteomics, computational biology, genomics, and bioinformatics; present data and contribute to project discussions; maintain clear records and internal reports; and may have opportunities to contribute to manuscripts and external presentations. Regeneron describes its total rewards package as potentially including annual bonuses or other incentives, equity awards, retirement benefits, health and wellness programs, insurance, paid time off, and family support benefits, depending on country and role. Many roles are required to be performed on-site; applicants should confirm expectations for this role and location with the recruiter or hiring manager.

Requirements

• A master's degree in analytical chemistry, biochemistry, molecular biology, biology, bioinformatics, or a related discipline with approximately 2–4 years of relevant laboratory experience; alternatively, a bachelor's degree in a relevant discipline with approximately 4–6 years of laboratory experience. Relevant graduate research, co-op, or internship experience counts toward these ranges.
• Demonstrable wet-laboratory technique, including accurate pipetting and solution preparation, aseptic and contamination-aware practice, protocol adherence, and recording work performed.
• Coursework or practical experience in protein biochemistry, analytical chemistry, or molecular biology sufficient to understand the purpose of the relevant workflows.
• Comfort working with large data files and spreadsheets, and ability to maintain organized, well-documented records. Programming is not required.
• A record of careful, reproducible work and strong attention to detail.
• Ability to explain work performed and observations, and to work productively in a collaborative group.

Nice To Haves

• Hands-on LC-MS or mass-spectrometry experience in any application area, including proteomics, metabolomics, small molecules, or analytical quality control.
• Protein biochemistry techniques such as immunoprecipitation, affinity purification, Western blotting, cell culture, or tissue handling.
• Bottom-up proteomics sample preparation, including digestion and peptide cleanup.
• Exposure to proteomics data-analysis software such as PEAKS, FragPipe, Proteome Discoverer, or Spectronaut.
• Background in immunology, particularly HLA/MHC antigen presentation.
• Any Python or R scripting experience, including informal work in a class, thesis, or previous job.
• Curiosity about machine learning applied to scientific data or reproducible analysis pipelines such as Nextflow, nf-core, or containerized workflows; experience is a bonus, not a requirement.
• Prior experience in a biotech, pharmaceutical, CRO, academic core-facility, or university research laboratory.

Responsibilities

• Prepare samples for bottom-up proteomics, including cell and tissue lysis, enzymatic digestion, peptide cleanup, enrichment, and fractionation.
• Perform immunoprecipitation and affinity-enrichment workflows, progressing from guided work to independent execution.
• Maintain sample tracking, run records, reagent logs, and quality-control records so datasets remain interpretable and auditable.
• Support laboratory operations, including reagent preparation, inventory, instrument housekeeping, and safety compliance.
• Acquire LC-MS/MS data on high-resolution instrumentation, initially under supervision and increasingly independently.
• Perform routine instrument maintenance, calibration, performance checks, and first-line troubleshooting.
• Contribute to method optimization, particularly for low-abundance analytes.
• Process mass-spectrometry data using established database-search workflows and apply appropriate false-discovery control.
• Review, filter, and summarize results, assessing whether identifications are adequately supported.
• Help search mass-spectrometry data against custom protein sequence databases derived from RNA-seq, ribosome profiling, and long-read transcriptome data, and learn how those databases are built and curated.
• Optionally take on scripted analysis in Python or R as interest and experience develop.
• Present data at group meetings and contribute to project-team discussions.
• Collaborate with colleagues across proteomics, computational biology, genomics, and bioinformatics.
• Maintain clear written records and contribute to internal reports, with opportunities to contribute to manuscripts and external presentations.
• Raise questions and problems promptly.

Benefits

• Competitive total rewards package may include annual bonuses or other incentive plans, equity awards, pension or retirement benefits, 401(k) company match, health and wellness programs, fitness centers, medical, dental, vision, life and disability insurance, paid time off, and family support benefits, depending on country and role.

What This Job Offers

• Job Type: Full-time
• Career Level: Senior