Senior Associate Scientist - Proteogenomic & Immunopeptidomics

Regeneron Pharmaceuticals • Tarrytown, GA

1d • $80,300 - $131,100 • Onsite

About The Position

Regeneron is seeking a hands-on Senior Associate Scientist to join a translational proteomics group focused on discovering and validating novel cell-surface and HLA-presented antigens for therapeutic antibody, bispecific, and cell-therapy programs. The role combines proteogenomics and immunopeptidomics, using high-sensitivity LC-MS/MS to develop peptide-level evidence into validated target candidates. It is based onsite in Tarrytown, New York.

This role is designed for someone with solid laboratory fundamentals and a strong interest in learning mass spectrometry. Prior expertise in immunopeptidomics or proteogenomics is not expected; structured, hands-on training is provided by experienced scientists as part of project work. A master's degree is a strong fit, and bachelor's-level candidates with relevant laboratory experience are welcome. The role offers scope to build technical independence and, if interested, develop computational skills alongside core bench work.

Training during the first year may include operating, calibrating, maintaining, and troubleshooting Thermo Orbitrap and Bruker timsTOF mass spectrometers; handling nanoflow liquid chromatography columns and emitters; HLA class I and II immunoprecipitation; proteomics database searching and false-discovery control; and targeted PRM/MRM assays using stable isotope-labeled peptide standards. Programming is not required, though there is an opportunity to learn Python or R scripting and computational analysis approaches such as machine-learning tools and reproducible pipelines.

The position requires approximately 2–4 years of relevant laboratory experience with a relevant master's degree, or approximately 4–6 years with a relevant bachelor's degree. Relevant graduate research, co-op, or internship experience counts toward those ranges. The stated annual salary range is $80,300 to $131,100. Regeneron describes a competitive total rewards package that may include annual bonuses or other incentives, equity awards, retirement benefits, health and wellness programs, insurance, paid time off, and family support benefits; offerings depend on country and role.

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; or 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, solution preparation, aseptic and contamination-aware practice, following protocols, and recording work accurately.
• 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 the ability to maintain organized, well-documented records; programming is not required.
• A track 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 QC.
• 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.
• Immunology background, particularly HLA/MHC antigen presentation.
• Any Python or R scripting experience, including informal scripts written for a class, thesis, or previous job; deep expertise is not expected.
• Interest in 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.
• Experience in a biotech, pharmaceutical, CRO, academic core-facility, or university research laboratory setting.

Responsibilities

• Prepare samples for bottom-up proteomics, including cell and tissue lysis, enzymatic digestion, peptide cleanup, enrichment, and fractionation, with attention to low-input samples.
• Perform immunoprecipitation and affinity enrichment workflows, initially under guidance and progressing toward independent execution.
• Maintain sample tracking, run records, reagent logs, and quality-control practices to keep datasets interpretable and auditable.
• Support general laboratory operations, including reagent preparation, inventory, instrument housekeeping, and safety compliance.
• Acquire LC-MS/MS data using high-resolution instrumentation, initially with supervision and increasingly independently.
• Learn and perform routine instrument maintenance, calibration, performance checks, and first-line troubleshooting.
• Contribute to method optimization, particularly for low-abundance analytes, as understanding of the platform develops.
• Process mass spectrometry data using established database-search workflows and apply appropriate false-discovery control.
• Review, filter, and summarize results, developing judgment to identify poorly supported identifications.
• 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.
• Take on scripted analysis in Python or R if interested, as experience develops.
• Present data at group meetings and contribute to project-team discussions.
• Collaborate with colleagues across proteomics, computational biology, genomics, and bioinformatics.
• Keep clear written records and contribute to internal reports, with opportunities to contribute to manuscripts and external presentations.
• Raise problems promptly and ask questions when needed.

Benefits

• Annual bonuses or other incentive plans may be included, depending on country and role.
• Equity awards may be included, depending on country and role.
• Pension or retirement benefits may be included, depending on country and role.
• 401(k) company match may be included, depending on country and role.
• Health and wellness programs may be included, depending on country and role.
• Fitness centers may be available, depending on country and role.
• Insurance benefits, including medical, dental, vision, life, and disability coverage, may be included, depending on country and role.
• Paid time off may be included, depending on country and role.
• Family support benefits may be included, depending on country and role.

What This Job Offers

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