Proteomics Scientist

Proxima; Boston; On-site; PHP 7,402,837 - 10,487,352; Full time

Job summary

Proxima seeks a Proteomics Scientist to build NeoLink workflows and drive data generation for internal programs. This on-site Boston role targets individuals entering industry from XLMS or chemical proteomics, with hands-on mass spectrometry and proteomics expertise.

The candidate will collaborate with computational biologists and ML scientists to design experiments and ensure high-quality data while maintaining LC/MS instrumentation in a fast-paced environment.

Qualifications

• PhD or postdoc in XLMS or chemical proteomics; ready to move into industry.
• Experience with LC/MS workflows and instrumentation.
• Strong documentation and data presentation skills.

Responsibilities

• Design, optimize and execute structural and chemical proteomic workflows (cross-linking, affinity purification, proximity biotinylation, ligandability profiling).
• Collaborate with computational biologists and ML scientists to design experiments yielding high-quality, analyzable data.
• Maintain, operate, and coordinate the use of LC/MS instruments.

Skills

Sample prep (MS-proteomics)

Structural proteomics

Chemical proteomics

LC/MS operation

Proteomics data analysis

English communication

Education

PhD or postdoc in XLMS or chemical proteomics

Tools

Thermo Fisher Neo Vanquish

Orbitrap mass spectrometers

Job description

Proteomics Scientist

Location: This role is based in-person at our Boston lab, MA. We're not able to support remote or hybrid arrangements for this position.

Candidates currently completing a PhD or postdoc in an XLMS or chemical proteomics lab are welcome to apply - we're interested in talent about to graduate and looking to move into industry.

About Proxima

Proxima (formerly VantAI) is discovering the next generation of proximity therapeutics by making protein interactions programmable. Our platform brings together frontier AI models, 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 with an elite group of VCs including DCVC, NVIDIA’s NVentures, AIX, Yosemite among others.

Neo is our all-atom foundation model that combines state-of-the-art structure prediction and molecular generation in a single system. Neo 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, we are developing an advanced structural interactomics platform NeoLink built on proprietary proteomics technology and a lab equipped with next-generation mass spectrometry instrumentation. This platform produces proteome-scale maps of protein interactions and identifies small molecules that modulate proximity. Together with Neo, it creates an integrated system capable of co-folding protein complexes while generating candidate small molecules to influence those interactions.

Proximity-based therapeutics represent one of the most promising frontiers in modern drug discovery with the potential to treat previously intractable diseases and target ‘undruggable’ proteins. We’re building the tech and the team to make that happen. Come join us!

About the Role

NeoLink is Neo’s bridge to the physical world: we leverage proteomics to directly assay molecular interactions at an amino‑acid level of resolution, enabling a feedback loop where machine‑learning models directly explore and learn from biology. As a Proteomics Scientist, you will play a critical role in building out NeoLink and advancing critical R&D workflows for data generation and internal programs.

Your tasks and responsibilities

• Design, optimize and execute the structural and chemical proteomic workflows (cross‑linking, affinity purification, proximity biotinylation, ligandability profiling) that form the core of NeoLink
• Partner with computational biologists and machine learning scientists to design experiments that produce high‑quality, analysis‑ready data.
• Maintain, operate, and coordinate the usage of LC/MS instruments

Your skills

• Excellent sample preparation skills for mass spectrometry‑based proteomics
• Experience in structural proteomics (cross‑linking, covalent footprinting) or chemical proteomics (activity/affinity‑based protein profiling, affinity selection)
• Comfort operating in a fast‑paced, results‑oriented environment
• Expertise in handling and maintaining LC and MS instruments, in particular Thermo Fisher Neo Vanquish LC systems and Orbitrap or Astral mass spectrometers.
• Knowledge of proteomic data analysis methods and software toolsAbility to accurately and reliably document and present scientific data
• Strong communication skills and proficiency in English