Scientist, Mass Spectrometry

Axiom•South San Francisco, CA

About The Position

Axiom is hiring a Scientist, Mass Spectrometry to own its LC-MS/MS operations across targeted and untargeted workflows. The role supports Axiom’s human liver safety platform, which combines advanced human cell systems with imaging, transcriptomics, mass spectrometry, and drug metabolism measurements to investigate drug toxicity and predict human drug outcomes. The scientist will develop and run experiments to identify drug metabolites and reactive intermediates, measure drug-related changes in cellular metabolism, and establish proteomics workflows. They will generate high-quality reference datasets, qualify analytical methods, maintain instrument reliability, and work with computational scientists and engineers to turn experiments into benchmarks and AI-enabled laboratory workflows. The position calls for close collaboration across analytical chemistry, biology, computation, and engineering, as well as strong ownership of data quality and dependable laboratory practices.

Requirements

Exceptional hands-on LC-MS/MS expertise and a 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 true 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 on automation, adaptive methods, and closed-loop experimentation.
End-to-end ownership, including identifying priorities, moving from observation to action, and following problems through to verified resolution.
High standards for sample handling, reproducibility, documentation, and data quality.
Clear communication, generosity with expertise, and curiosity about work across analytical chemistry, biology, computation, and engineering.
Technical capability in LC-MS/MS operation and method development, including UHPLC, UV detection, high-resolution MS, and fragmentation methods.
Technical capability in instrument troubleshooting, preventive maintenance, vacuum systems, nitrogen generators, and sample preparation equipment.
Technical capability in reactive-metabolite trapping, metabolic incubations, stable-isotope labeling, and metabolite identification.
Technical capability in targeted and untargeted metabolomics, including extraction, chromatographic separation, and analysis of complex biological matrices.
Technical capability in proteomics sample preparation, protein digestion, peptide separation, and LC-MS/MS acquisition.
Technical capability in assay development and qualification, calibration, internal standards, matrix effects, recovery, carryover, and measurement uncertainty.
Technical capability in spectral interpretation, accurate-mass analysis, isotope patterns, adduct identification, and integrating LC-MS/MS with UV and NMR evidence.
Technical capability in experimental data analysis using vendor software and tools such as MZmine, OpenMS, MS-DIAL, Skyline, or SIRIUS.

Nice To Haves

Python or R experience.
Experience with laboratory automation, instrument interfaces, and 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 that reveal how drugs alter cellular metabolism and connect measurements with imaging, transcriptomics, and other indicators of toxicity.
Establish proteomics workflows with biology and computational teams, from sample preparation and digestion through peptide separation and LC-MS/MS acquisition.
Generate 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 with controls, calibration, and acceptance criteria for sensitivity, selectivity, reproducibility, carryover, and matrix effects.
Partner with computational scientists to create 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 QC, 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.
Maintain exacting standards for sample handling, reproducibility, documentation, and data quality, and train technicians and build dependable laboratory practices.
Communicate clearly and collaborate across analytical chemistry, biology, computation, and engineering.