Sr./Principal Analytical Scientist - Mass Spectrometry

QuantumCell; South San Francisco (CA); On-site; USD 180,000 - 240,000; Full time

Benefits offered by this job

Competitive compensation

Equity opportunity

Conference support

Job summary

QuantumCell is building a groundbreaking mass-spectrometry-enabled proteomics platform to decode neuronal protein networks. We seek a Senior/Principal Analytical Scientist to own the MS function from instrument procurement to automated operation, interfacing analytical chemistry, cell biology, automation, and AI teams.

You will lead method development, high-throughput workflows, and data analysis collaboration, shaping data for AI models and Virtual Cell.

Qualifications

• Ph.D. in Analytical Chemistry, Biochemistry, Proteomics, Chemical Biology, or a closely related discipline.
• 5+ years hands-on experience operating high-resolution MS
• Expert-level proficiency with Orbitrap-based and/or TIMS-based instruments
• Expert command of nanoflow and microflow LC-MS/MS
• Hands-on experience with quantitative proteomics strategies (TMT, LFQ, SILAC) and differential abundance analysis
• Proficiency with major proteomics data analysis platforms
• Strong quantitative and data literacy; able to engage with bioinformatics and AI teams on data structures, quality metrics, and statistical models

Responsibilities

• Lead instrument market evaluation for neuronal protein profiling.
• Define vendor-neutral MS specifications and procurement.
• Oversee MS lab facility layout and safety for neuronal lysates.
• Develop high-throughput proteomics workflows for comparing genotypes.
• Collaborate with automation engineers to integrate MS with robotics.
• Own MS data processing and contribute to AI-ready datasets.
• Mentor junior scientists and contribute to IP/publications

Skills

Mass spectrometry-based proteomics

Orbitrap/ TIMS instruments

Nanoflow LC-MS/MS

Quantitative proteomics (TMT, LFQ, SIL

Education

Ph.D. in Analytical Chemistry/Biochemistry/Proteomics

Tools

Spectronaut

DIA-NN/OpenSWATH

LIMS integration

Job description

At QuantumCell, we are rewriting the rules of drug discovery — and we're just getting started. We are a dynamic tech company in the biology space on a mission to decode and defeat the most complex brain disorders of our time. By converging next-generation sensing technologies, autonomous robotics, and cutting-edge AI, we are building the world's first high-fidelity virtual cell and virtual system model: a mechanistically anchored simulation of human biology that can predict how drugs will behave in a patient before a single trial is run.

Anchored by world-class scientific partnerships and access to elite computational infrastructure, we generate new types of biological data at a scale and resolution that no one has achieved before. This isn't incremental science. It's a fundamental shift from reductionist biology to a true systems-level understanding of the human brain — and we are looking for bold, brilliant people to help us build it!

The Role

We are seeking a Senior or Principal Analytical Scientist with deep, hands‑on expertise in mass spectrometry‑based proteomics to own our MS function end‑to‑end — from instrument selection and procurement through day‑to‑day operations, method development, and integration into our automated robotic discovery platform.

This is a foundational role. You will be the leading authority on mass spectrometry at QuantumCell, responsible for standing up a best‑in‑class MS capability purpose‑built for high‑throughput protein profiling in neurons. You will work at the interface of analytical chemistry, cell biology, automation engineering, and informatics, and your data will feed directly into the AI models underpinning our Virtual Cell.

If you have built high‑throughput MS‑based proteomic workflows from scratch, know the instrument landscape inside out, and want your science to matter at the level of drug discovery and patient outcomes — this role was designed for you.

What You Will Do

Instrument Selection, Procurement & Facility Setup

Lead a rigorous, needs‑based evaluation of the current mass spectrometer market against QuantumCell's throughput, sensitivity, and automation requirements for neuronal protein profiling.

Define vendor‑neutral technical specifications covering mass accuracy, resolving power, scan speed, dynamic range, ion mobility capability, and compatibility with nano‑/micro‑flow LC and robotic sample introduction.

Manage the full procurement lifecycle: Vendor demonstrations and benchmarking with QuantumCell‑relevant samples, contract negotiation, installation, and qualification.

Design and oversee the physical layout of the MS laboratory, including LC infrastructure, gas supplies, UPS, vibration isolation, environmental controls, and biosafety requirements for neuronal lysate samples.

Establish spare‑parts inventory, service contracts, and vendor escalation protocols to maintain instrument uptime for high‑throughput operations.

Method Development — PPI & Proteomics Workflows

Establish robust quantitative proteomics workflows enabling direct comparison of protein networks across neuronal genotypes, perturbation conditions, and disease states.

Optimize chromatographic methods (nanoflow, microflow, short‑gradient high‑throughput approaches) to balance depth of proteome coverage with sample throughput demands imposed by high‑content screening formats.

Develop and validate targeted MS assays for the rapid quantification of specific high‑priority interaction partners emerging from discovery screens.

Automated High‑Throughput Operations

Collaborate directly with automation engineers to integrate the mass spectrometer and its LC front‑end into QuantumCell's robotic systems, enabling automated sample preparation, plate‑to‑vial transfer, and injection queue management at a throughput and reliability level that supports continuous, unattended production runs rather than batch‑limited operation.

Define and validate the robotic sample‑preparation workflow from automated cell lysis, on‑robot enrichment, and digestion through LC loading, engineering each step for run‑to‑run reproducibility so that data quality holds constant as sample volume scales from validation runs to full production throughput.

Specify and validate robotic‑compatible sample containers, plate formats, and consumables suitable for automated handling on liquid handlers, standardizing formats across workcells so consumable and labware choices don't become a bottleneck as capacity expands.

Work with software engineers to implement bidirectional data flow between the MS instrument software and QuantumCell's data pipeline, preserving sample tracking integrity from cell plate to peptide spectrum at the barcode level: the traceability backbone that makes every dataset audit‑ready and trustworthy as an ML training input.

Establish automated QC checkpoints (injection standards, system suitability tests) that trigger on‑robot decisions and flag off‑specification runs without human intervention, so quality control scales with throughput instead of requiring proportionally more manual oversight as run volume grows.

Plan and specify the MS capacity roadmap, including additional instruments, parallel injection lines, and integration points for future workcell expansion, so throughput scale‑up is a procurement and validation exercise rather than a workflow redesign.

Data Analysis & Bioinformatics Collaboration

Own MS raw data processing and protein identification pipelines using best‑in‑class tools and contribute to their adaptation for high‑throughput automated runs.

Partner closely with the computational biology and AI teams to deliver clean, structured, annotated proteomics datasets that integrate into the protein network models and Virtual Cell framework.

Develop QC metrics and data dashboards enabling rapid, real‑time assessment of run quality, proteome depth, and reproducibility across the robotic system.

Scientific Leadership & External Engagement

Serve as the internal authority and go‑to expert on all things mass spectrometry, providing guidance to biologists, automation engineers, and computational scientists on best practices and experimental design.

Stay at the forefront of the rapidly evolving proteomics field; evaluate and adopt emerging technologies (data‑independent acquisition (DIA), ion mobility, single‑cell proteomics)

Contribute to intellectual property generation, scientific publications, and presentations at major proteomics and drug discovery conferences.

Mentor junior scientists and help build the broader analytical sciences function as the company scales.

What You Will Bring

Required Qualifications

• Ph.D. in Analytical Chemistry, Biochemistry, Proteomics, Chemical Biology, or a closely related discipline, with deep experience in mass spectrometry‑based proteomics.
• 5+ years of hands‑on experience operating and developing methods on high‑resolution mass spectrometers, with demonstrated ownership.
• Expert‑level proficiency with Orbitrap‑based instruments and/or TIMS‑based instruments; ability to tune, calibrate, and troubleshoot at the hardware level.
• Expert command of nanoflow and microflow LC‑MS/MS, including column chemistry, gradient optimization, and chromatographic troubleshooting.
• Hands‑on experience with quantitative proteomics strategies (TMT, LFQ, SILAC) and the statistical workflows required for differential abundance analysis.
• Proficiency with major proteomics data analysis platforms.
• Strong quantitative and data literacy; able to engage meaningfully with bioinformatics and AI teams on data structures, quality metrics, and statistical models.

Preferred Qualifications

Experience designing or operating automated sample‑preparation workflows for proteomics in conjunction with liquid handling robotics.

Direct involvement in integrating mass spectrometers or LC systems with laboratory automation platforms (scheduling software, LIMS, robotic sample handlers).

Experience with DIA acquisition strategies and DIA‑specific analysis tools (Spectronaut, DIA‑NN, OpenSWATH).

Familiarity with single‑cell or ultra‑low‑input proteomics (nanoSPE, microPOTS, SCoPE‑MS).

Background in neurobiology, iPSC‑derived neuronal models, or CNS drug discovery is a meaningful plus.

Prior experience in a startup or early‑stage biotech; comfort building a function from the ground up with limited precedent.

What We Offer

• Competitive compensation package (salary, equity, bonus) based on experience.
• Access to world‑class scientific collaborators and leading computational infrastructure, including large‑scale GPU clusters and proprietary biological datasets of exceptional scale and resolution.
• A unique opportunity to help define how AI learns from biology at one of the most ambitious companies in CNS drug discovery.
• The chance to contribute to a deeply mission‑driven organization focused on transforming patient outcomes and advancing treatments for complex diseases.
• Support for conference attendance and active participation in the scientific community.
• A collaborative, inclusive, and fun culture where you’ll play a key role in building the team, shaping the environment, and driving meaningful impact from the ground up.