Senior Research Associate

Proxima; Boston; On-site; PHP 4,810,583 - 6,614,551; Full time

Job summary

Proxima in Boston is looking for a Contract Senior Research Associate to work on cross-linking mass spectrometry (XLMS) for their NeoLink Platform. You will execute XLMS experiments from end to end, prepare protein samples, and collaborate with a team of scientists to develop a cutting-edge structural interactomics platform. A Bachelor's/Master's in a related scientific discipline and 5+ years of relevant industry experience are essential for this role. Strong troubleshooting skills and proficiency in mass spectrometry are required. The company is engaged in advanced drug discovery techniques.

Qualifications

• 5+ years of hands-on industry experience in drug discovery, proteomics, or analytical chemistry.
• Demonstrated proficiency in mass spectrometry workflows.
• Ability to manage multiple experiments and timelines independently.

Responsibilities

• Execute XLMS experiments including protein sample preparation and LC-MS data acquisition.
• Operate and maintain HPLC and LC-MS systems.
• Collaborate with scientists to integrate XLMS data into workflows.

Skills

Mass spectrometry workflows

HPLC experience

Protein purification

Troubleshooting skills

Strong record keeping

Education

Bachelor's/Master's in Biochemistry, Chemistry, or Biology

Tools

LC-MS

HPLC systems

Job description

Team: NeoLink Platform

Location: Boston, MA

Employment Type: Contract

About Proxima

Proxima (formerly VantAI) is advancing an AI-native approach to drug discovery by making protein interactions programmable. Our platform brings together foundation-model machine learning, a scalable data generation engine, and a partnership track record exceeding $5B in collaborations across the world's leading biopharma and tech organizations. We've recently closed an oversubscribed seed round partnering us with an elite group of sophisticated and dedicated VCs including DCVC, Nvidia's Nventures, AIX, Yosemite among others.

Neo-1 is our all-atom foundation model that combines state-of-the‑art structure prediction and molecular generation in a single system. Neo-1 enables rapid exploration of chemical and structural space for high value, previously intractable targets, and in particular unlocks small molecule proximity therapeutics like molecular glues with AI for the first time.

In parallel, Proxima is developing an advanced structural interactomics platform built on proprietary cross‑linking mass spectrometry (XLMS) technology and a lab equipped with next‑generation mass spectrometry instrumentation. This platform produces proteome‑scale interactome maps and helps identify small molecules that modulate protein interactions. Together with Neo‑1, it creates an integrated system capable of co‑folding protein complexes while also generating candidate small molecules to influence those interactions.

Based on these proprietary capabilities, Proxima is developing a robust pipeline of first‑in‑class medicines across several therapeutic areas including immunology and inflammation, cardiometabolic and aggregate‑driven diseases. The company is currently advancing multiple assets through preclinical development that address both novel and well validated targets.

About the Role

We are seeking a hands‑on Contract Senior Research Associate to join the NeoLink Platform team and drive execution of cross‑linking mass spectrometry (XLMS) experiments that fuel Proxima's structural interactomics platform. This role will focus on running XLMS sample preparation and LC‑MS workflows end‑to‑end, learning routine maintenance of our next‑generation mass spectrometry instrumentation, and contributing to the scale‑up of proteome‑wide interaction mapping. You will work closely with proteomics scientists, computational biologists, and chemists to generate the proprietary XLMS data that trains Neo‑1 and powers our drug discovery pipeline.

What You’ll Do

• Execute XLMS experiments end‑to‑end, including protein sample preparation, crosslinking reactions, and LC‑MS data acquisition

• Operate and maintain HPLC and LC‑MS systems; learn routine instrument maintenance including column installation, source cleaning, calibration, and system performance QC

• Perform protein expression and purification (bacterial and mammalian systems) to support XLMS substrate preparation

• Troubleshoot experimental and instrument issues and contribute to continuous improvement of sample preparation workflows

• Maintain accurate experimental records in the electronic lab notebook and adhere to strong documentation standards

• Support platform scale‑up by writing and refining SOPs, training teammates, and identifying automation opportunities

• Collaborate closely with computational biologists, chemists, and other scientists to integrate XLMS data into structural biology and drug discovery workflows

Must Haves

• Bachelor's/Masters degree in Biochemistry, Chemistry, Biology, or a related scientific discipline

• 5+ years of hands‑on industry experience in a drug discovery, proteomics, or analytical chemistry setting

• Demonstrated proficiency in mass spectrometry workflows, with hands‑on LC‑MS experience required

• Hands‑on HPLC experience, including method setup, column selection maintenance, and troubleshooting

• Protein purification experience (e.g., Ni‑NTA affinity chromatography, size‑exclusion chromatography, ion exchange; AKTA or equivalent FPLC systems)

• Strong troubleshooting skills and excellent attention to detail

• Ability to manage multiple experiments and timelines independently in a fast‑paced environment

• Excellent organizational skills with strong record keeping

Nice to Haves

• PhD in a relevant discipline (biochemistry, analytical chemistry, chemical biology, structural biology)

• Prior experience with cross‑linking mass spectrometry (XLMS) workflows

• Experience operating Orbitrap‑class instruments (Astral, Exploris, Eclipse, or similar)

• Familiarity with proteomics data analysis tools (e.g., Scout, xiSEARCH, Proteome Discoverer, MaxQuant, Skyline)

• Experience with click chemistry enrichment and affinity‑tag‑based peptide capture

• Experience with automated sample preparation platforms (e.g., Hamilton, Opentrons)

• Familiarity with SEC fractionation, SP3 sample prep, or crosslinker chemistry optimization

• Prior biotech or pharmaceutical industry experience in a platform or drug discovery environment