Scientist III – Mass Spectrometry / Proteomics

ThermoFisher Scientific; Rockford (IL); On-site; USD 83,000 - 139,000; Full time

Benefits offered by this job

Medical and dental plans

Vision plan

Employee assistance programs

Paid time off 120 hours

Retirement plan (401(k))

Employee stock purchase plan

Tuition reimbursement

Job summary

Thermo Fisher Scientific in Illinois seeks a Scientist III – Mass Spectrometry / Proteomics to develop automated sample preparation workflows and LC-MS methods for proteomics. You’ll design experiments, optimize workflows, analyze data, and translate results into scalable processes.

Working cross-functionally with scientists, engineers, and management, you’ll contribute to method development, validation, and technology transfer, while communicating results and recommendations to project teams.

Qualifications

• PhD, MS with 3+ years, or BS with 5+ years in biochemistry, analytical chemistry, proteomics or related field.
• Hands-on experience with proteomics and MS sample prep workflows.
• Experience with LC-MS data acquisition/analysis and protein biochemistry.
• Basic programming/scripting for data analysis (Python/R).
• Strong experimental design and problem-solving skills.

Responsibilities

• Design and execute experiments for MS sample prep and workflow development.
• Develop and optimize MS sample prep methods for LC-MS analysis.
• Create automated, high-throughput sample prep workflows.
• Translate manual methods into automated workflows.
• Evaluate workflow performance using LC-MS and quantitative proteomics.
• Analyze MS data to assess workflow performance.
• Apply bioinformatics, statistics, or programming for data analysis.
• Troubleshoot challenges and improve workflow robustness and throughput.
• Contribute to new product development, validation, and technology transfer.
• Collaborate with cross-functional teams to meet milestones.
• Prepare technical docs, protocols, and presentations.

Skills

Proteomics workflows

Mass spectrometry

Experimental design

Troubleshooting

Data analysis

Collaboration

Education

PhD in Biochemistry/Proteomics

MS +3 years experience

BS +5 years experience

Tools

Thermo Scientific LC-MS systems

LC-MS software

Python

R

Job description

Work Schedule

Standard (Mon-Fri)

Environmental Conditions

Able to lift 40 lbs. without assistance, Cold Room/Freezers -22degreesF/-6degrees C, Laboratory Setting, Some degree of PPE (Personal Protective Equipment) required (safety glasses, gowning, gloves, lab coat, ear plugs etc.), Will work with hazardous/toxic materials

Job Description

About Thermo Fisher Scientific

As part of the Thermo Fisher Scientific team, you’ll discover meaningful work that makes a positive impact on a global scale. Join our colleagues in bringing our Mission to life every day to enable our customers to make the world healthier, cleaner, and safer. We provide our global teams with the resources needed to achieve individual career goals while helping take science a step beyond by developing solutions to some of the world’s toughest challenges.

DESCRIPTION

We are seeking a highly motivated Scientist III – Mass Spectrometry / Proteomics to join our R&D team. This role will focus on developing innovative sample preparation methods and automated workflows for mass spectrometry-based proteomics. The successful candidate will apply expertise in protein biochemistry, proteomics, MS sample preparation, and LC-MS analysis to develop and evaluate new workflows and technologies. A key focus will be the development and automation of robust, reproducible sample preparation methods, including workflows for limited and challenging biological samples. You will design and execute experiments, optimize sample preparation and automated workflows, analyze MS data, and troubleshoot technical challenges. Working in a cross-functional environment, you will collaborate with scientists, engineers, automation teams, Product Management, Manufacturing, and other functions to translate scientific concepts into practical and scalable workflows.

Key Responsibilities

• Design and execute experiments supporting MS sample preparation and workflow development for proteomics.
• Develop and optimize MS sample preparation methods for LC-MS analysis.
• Develop, optimize, and evaluate automated and high-throughput sample preparation workflows.
• Translate manual sample preparation methods into robust, reproducible automated workflows.
• Evaluate workflow performance using LC-MS and quantitative proteomics approaches.
• Process, analyze, and interpret MS data to assess workflow performance.
• Apply basic bioinformatics, statistical, or programming approaches to support data analysis and visualization.
• Troubleshoot technical challenges and improve workflow sensitivity, robustness, reproducibility, and throughput.
• Contribute to new product and technology development activities, including feasibility studies, method development, testing, validation, and technology transfer.
• Collaborate with cross-functional teams to achieve technical milestones and project objectives.
• Prepare technical documentation, experimental reports, protocols, and presentations.
• Communicate scientific results and recommendations to project teams and stakeholders.

Qualifications

• Recent Ph.D. graduates, M.S. with 3 + years , or B.S. with 5+ years of relevant experience in Biochemistry, Analytical Chemistry, Chemistry, Proteomics, Mass Spectrometry, Bioinformatics, or a related scientific discipline.
• Hands-on experience with proteomics and MS sample preparation workflows.
• Experience with protein biochemistry and sample preparation techniques such as protein extraction, reduction/alkylation, digestion, labeling, cleanup, or enrichment.
• Experience with LC-MS-based proteomics data acquisition and/or analysis.
• Basic experience with Python, R, or other programming/scripting tools for scientific data analysis, visualization, or workflow support.
• Familiarity with bioinformatics and statistical analysis of proteomics data.
• Strong experimental design, analytical, troubleshooting, and scientific problem-solving skills.
• Ability to independently plan, execute, document, and interpret scientific experiments.
• Strong written and verbal communication skills and ability to work effectively in a multidisciplinary team environment.

Preferred Qualifications

• Experience developing or implementing automated or high-throughput sample preparation workflows, including liquid-handling platforms.
• Experience translating manual laboratory workflows into automated methods.
• Experience with low-input, limited, or challenging biological samples, including single-cell or low-cell-number proteomics and FFPE tissue samples.
• Experience developing sample preparation methods optimized for post-translational modifications (PTMs) analysis.
• Experience with Thermo Scientific LC-MS systems and associated software.
• Experience with quantitative proteomics workflows and analysis of complex MS datasets.
• Experience with product development, method validation, design transfer, or technology transfer.
• Scientific publications, conference presentations, patents, or other demonstrated research contributions.

Compensation and Benefits

The salary range estimated for this position based in Illinois is $83,300.00–$138,900.00.

This position may also be eligible to receive a variable annual bonus based on company, team, and/or individual performance results in accordance with company policy. We offer a comprehensive Total Rewards package that our U.S. colleagues and their families can count on, which includes:

• A choice of national medical and dental plans, and a national vision plan, including health incentive programs
• Employee assistance and family support programs, including commuter benefits and tuition reimbursement
• At least 120 hours paid time off (PTO), 10 paid holidays annually, paid parental leave (3 weeks for bonding and 8 weeks for caregiver leave), accident and life insurance, and short- and long-term disability in accordance with company policy
• Retirement and savings programs, such as our competitive 401(k) U.S. retirement savings plan
• Employees’ Stock Purchase Plan (ESPP) offers eligible colleagues the opportunity to purchase company stock at a discount

For more information on our benefits, please visit: https://jobs.thermofisher.com/global/en/total-rewards

Thermo Fisher Scientific is an EEO/Affirmative Action Employer and does not discriminate on the basis of race, color, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability or any other legally protected status.