Associate Scientist Discovery Proteomics

Biopharma Careers; South San Francisco (CA); On-site; USD 90,000 - 130,000; Full time

Job summary

Amgen in South San Francisco seeks an Associate Scientist Discovery Proteomics to advance LC-MS/MS-based research for early discovery projects. You will execute quantitative proteomic workflows to support cell-surface target discovery, proximity labeling, and biomarker studies, collaborating with proteomics, biology, automation, and bioinformatics teams.

The role emphasizes high-quality data generation, rigorous analysis, and cross-functional communication in a fast-paced environment, with

Qualifications

• Master’s degree or higher in analytical chemistry, biochemistry, chemical biology, molecular/cell biology, or related field.
• Hands-on experience with proteomic sample preparation and LC-MS workflows.
• Familiarity with proteomics software (Proteome Discoverer, Spectronaut, DIA-NN).
• Experience with protein enrichment methods and LC-MS performance evaluation.

Responsibilities

• Execute and optimize established proteomics workflows for discovery and targeted approaches (DIA, TMT, label-free, PRM).
• Prepare samples from cell lines and biological matrices using cell-surface protein enrichment and proximity labeling.
• Operate LC-MS systems across vendor platforms, maintain instruments, troubleshoot issues with guidance from senior staff.
• Process and evaluate proteomic data with software and collaborate with bioinformatics to support analysis.
• Communicate plans, progress and results to team and cross-functional partners.
• Maintain detailed records of experiments, instrument performance, and analyses per data-integrity practices.

Skills

LC-MS/MS proteomics

Sample preparation

Data analysis

Communication

Education

Master’s degree

Bachelor’s degree and 2 years of scientific experience

Associate’s degree and 4 years of scientific experience

Tools

Proteome Discoverer

Spectronaut

DIA-NN

Proximity labeling

Tecan

Hamilton

Opentrons

KingFisher

Job description

Career Category

Scientific

Job Description

Join Amgen’s Mission of Serving Patients

At Amgen, if you feel like you’re part of something bigger, it’s because you are. Our shared mission, to serve patients living with serious illnesses, drives all that we do.

Since 1980, we’ve helped pioneer the world of biotech in our fight against the world’s toughest diseases. With our focus on four therapeutic areas –Oncology, Inflammation, General Medicine, and Rare Disease– we reach millions of patients each year. Amgen is advancing a broad and deep pipeline of medicines to treat cancer, heart disease, inflammatory conditions, rare diseases, and obesity and obesity-related conditions. As a member of the Amgen team, you’ll help make a lasting impact on the lives of patients as we research, manufacture, and deliver innovative medicines to help people live longer, fuller happier lives.

Our award-winning culture is collaborative, innovative, and science based. If you have a passion for challenges and the opportunities that lay within them, you’ll thrive as part of the Amgen team. Join us and transform the lives of patients while transforming your career.

Associate Scientist Discovery Proteomics

What you will do

Let’s do this. Let’s change the world. In this vital role you will expand your experience in liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics to work in South San Francisco. The team develops and applies proteomic technologies to support Amgen’s early discovery pipeline programs and technology platforms. In this role, the Associate Scientist will execute and optimize quantitative proteomic workflows supporting cell-surface target discovery, proximity-labeling studies, preclinical biomarker discovery, and mechanism-of-action investigations. The successful candidate will work closely with proteomics, functional genomics, biology, automation, and bioinformatics colleagues to generate high-quality, reproducible data and communicate results to project teams.

Responsibilities will include:

• 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, and 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.

What we expect of you

We are all different, yet we all use our unique contributions to serve patients. The] professional we seek is a scientist with these 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.
• Experience with automated sample‑preparation platforms, such as Tecan, Hamilton, Opentrons, or KingFisher, is a plus.
• Experience working with diverse biological sample types, including cell lines, tissues, biofluids, and FFPE specimens, is also preferred.
• Strong organizational, communication, and interpersonal skills, with attention to detail and a commitment to reliable, reproducible results.

What you can expect of us

The expected annual salary range for this role in the U.S. (excluding Puerto Rico) is posted. Actual salary will vary based on several factors including but not limited to, relevant skills, experience, and qualifications.

In addition to the base salary, Amgen offers a Total Rewards Plan, based on eligibility, comprising of health and welfare plans for staff and eligible dependents, financial plans with opportunities to save towards retirement or other goals, work/life balance, and career development opportunities that may include:

• A comprehensive employee benefits package, including a Retirement and Savings Plan with generous company contributions, group medical, dental and vision coverage, life and disability insurance, and flexible spending accounts
• A discretionary annual bonus program, or for field sales representatives, a sales‑based incentive plan
• Stock‑based long‑term incentives
• Award‑winning time‑off plans
• Flexible work models where possible. Refer to the Work Location Type in the job posting to see if this applies.

Application deadline

Amgen does not have an application deadline for this position; we will continue accepting applications until we receive a sufficient number or select a candidate for the position.

Sponsorship

Sponsorship for this role is not guaranteed.

In any materials you submit, you may redact or remove age‑identifying information such as age, date of birth, or dates of school attendance or graduation. You will not be penalized for redacting or removing this information.

As an organization dedicated to improving the quality of life for people around the world, Amgen fosters an inclusive environment of diverse, ethical, committed and highly accomplished people who respect each other and live the Amgen values to continue advancing science to serve patients. Together, we compete in the fight against serious disease.

Amgen is an Equal Opportunity employer and will consider all qualified applicants for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability status, or any other basis protected by applicable law.

We will ensure that individuals with disabilities are provided reasonable accommodation to participate in the job application or interview process, to perform essential job functions, and to receive other benefits and privileges of employment. Please contact us to request accommodation.

Salary Range

USD - USD