Scientist, Mass Spectrometry

Axiom•South San Francisco, CA

About The Position

Axiom is hiring a Scientist, Mass Spectrometry to build and operate its LC-MS/MS experiments for identifying drug metabolites, measuring changes in cellular metabolism and proteins, and investigating mechanisms of toxicity. The role combines analytical expertise with robotics and scientific AI to generate reliable data and help train models to predict human drug outcomes. Axiom’s high-throughput human liver safety platform brings together human cell systems, imaging, transcriptomics, mass spectrometry, and drug metabolism measurements. Its AI agents integrate experimental data with chemical structure, human exposure, and clinical reference compounds to predict whether drugs may be toxic in humans, why, and how they might be made safer. Axiom works with pharmaceutical companies and frontier AI labs to translate drug-safety discovery challenges and experimental feedback into training environments for AI systems. The scientist will own LC-MS/MS operations across targeted and untargeted workflows; develop reactive-metabolism, metabolomics, and proteomics experiments; qualify analytical methods; generate reference datasets; and partner with computational scientists and engineers to turn experiments into AI benchmarks and automated laboratory workflows. The role also includes maintaining instruments and supporting equipment, troubleshooting problems, managing consumables, and coordinating with service engineers.

Requirements

Exceptional hands-on LC-MS/MS expertise and deep understanding of chromatography, ionization, fragmentation, and targeted and untargeted analysis.
Experience developing and running reactive-metabolism, metabolomics, or proteomics experiments, with the ability to master unfamiliar workflows.
Strong experimental judgment, including designing controls, calibration strategies, and validation studies to distinguish genuine chemical and biological signals from contamination, interference, and instrument artifacts.
Ability to interpret complex spectra and mixtures, assess uncertainty, and recognize when molecular identification requires additional evidence.
Strong troubleshooting and maintenance skills, including resourcefulness in keeping instruments and supporting systems operating reliably.
Interest in developing experiments that teach AI agents to reason about chemistry and collaborating with engineers to automate quality control, adapt methods, and connect analysis with experimentation.
End-to-end ownership, including identifying priorities, acting quickly, and following problems through to verified resolution.
Exacting standards for sample handling, reproducibility, documentation, and data quality.
Clear communication, generosity in sharing expertise, and curiosity about working across analytical chemistry, biology, computation, and engineering.
LC-MS/MS operation and method development, including UHPLC, UV detection, high-resolution mass spectrometry, and fragmentation methods.
Instrument troubleshooting and preventive maintenance, including vacuum systems, nitrogen generators, and sample preparation equipment.
Reactive-metabolite trapping, metabolic incubations, stable-isotope labeling, and metabolite identification.
Targeted and untargeted metabolomics, including extraction, chromatographic separation, and analysis of complex biological matrices.
Proteomics sample preparation, protein digestion, peptide separation, and LC-MS/MS acquisition.
Assay development and qualification, calibration, internal standards, matrix effects, recovery, carryover, and measurement uncertainty.
Spectral interpretation, accurate-mass analysis, isotope patterns, adduct identification, and integration of LC-MS/MS with UV and NMR evidence.
Experimental data analysis using vendor software and tools such as MZmine, OpenMS, MS-DIAL, Skyline, or SIRIUS.

Nice To Haves

Python or R programming.
Experience with laboratory automation, instrument interfaces, or AI-assisted workflows for acquisition planning, quality control, and experimental analysis.

Responsibilities

Own LC-MS/MS operations across targeted and untargeted workflows, including chromatography, UV detection, mass spectrometry, and supporting equipment.
Develop and run reactive-metabolism assays to identify drug metabolites and trapped reactive intermediates, using isotope-labeled controls to verify signals and support structural interpretation.
Design metabolomics experiments to reveal drug-induced changes in cellular metabolism and connect measurements with imaging, transcriptomics, and other toxicity indicators.
Establish proteomics workflows with biology and computational teams, from sample preparation and digestion through peptide separation and LC-MS/MS acquisition.
Generate high-quality reference datasets from pure compounds and controlled mixtures, varying concentrations, matrices, chromatography, and fragmentation conditions to test molecular identification and quantification.
Develop and qualify methods using rigorous controls, calibration, and acceptance criteria for sensitivity, selectivity, reproducibility, carryover, and matrix effects.
Partner with computational scientists to convert experiments into benchmarks and training environments with experimentally verified answers for AI agents interpreting spectra, resolving mixtures, and investigating toxicity.
Work with engineers to integrate agents into real-time quality control, adaptive acquisition queues, method optimization, and lab-in-the-loop experiments.
Maximize instrument uptime through preventive maintenance, troubleshooting, user-serviceable repairs, consumables management, and coordination with service engineers.
Train technicians and build dependable laboratory practices.