Associate Scientist Discovery Proteomics

What You Will Do

• Expand experience in liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics.
• Execute and optimize quantitative proteomic workflows supporting:
• Cell-surface target discovery
• Proximity-labeling studies
• Preclinical biomarker discovery
• Mechanism-of-action investigations
• Work closely with proteomics, functional genomics, biology, automation, and bioinformatics colleagues.
• Generate high-quality, reproducible data and communicate results to project teams.
• Support Amgen’s preclinical pipeline through high-quality experimental execution and collaborative problem solving.

Key Responsibilities

• Execute and optimize established proteomics workflows, including sample preparation, peptide fractionation, liquid chromatography, and mass spectrometry acquisition for discovery and targeted approaches such as DIA, TMT, label-free DDA and PRM.
• Prepare samples from cell lines and other biological matrices using workflows such as cell-surface protein enrichment and proximity labeling.
• Operate LC-MS systems across several vendor platforms, assess instrument and data quality, perform routine maintenance, and troubleshoot common workflow or instrument issues with guidance from senior staff.
• Process and evaluate proteomic data using software such as Proteome Discoverer, Spectronaut, and DIA-NN.
• Work with bioinformatics and senior colleagues to support data analysis and sharing.
• Analyze results and identify technical issues in collaboration with project scientists.
• Communicate experimental plans, progress, and results to immediate team members and cross-functional collaborators.
• Maintain detailed and accurate records of experiments, protocols, instrument performance, and analyses in accordance with laboratory and data-integrity practices.

Requirements & Tech Stack

• LC-MS/MS-based proteomics
• Liquid chromatography
• Mass spectrometry acquisition
• DIA, TMT, label-free DDA, PRM
• Proteome Discoverer, Spectronaut, DIA-NN (or similar proteomics software)
• LC-MS systems
• Automated sample-preparation platforms (e.g., Tecan, Hamilton, Opentrons, or KingFisher) - a plus
• Diverse biological sample types (cell lines, tissues, biofluids, and FFPE specimens) - preferred

Qualifications

Basic Qualifications

• Master’s degree

OR

• Bachelor’s degree and 2 years of scientific experience

OR

• Associate’s degree and 4 years of scientific experience

OR

• High school diploma / GED and 6 years of scientific experience

Preferred Qualifications

• Bachelor’s, Master’s, or PhD degree in analytical chemistry, biochemistry, chemical biology, molecular or cell biology, or related discipline.
• Hands-on experience with proteomic sample preparation.
• Familiarity with Proteome Discoverer, Spectronaut, DIA-NN, or similar proteomics software and the ability to assess data quality and interpret results.
• Experience with protein enrichment methods is desirable.
• Ability to evaluate LC-MS performance and troubleshoot routine sample-preparation, chromatography, or instrument issues.
• Strong organizational, communication, and interpersonal skills, with attention to detail and a commitment to reliable, reproducible results.