Scientific Engineering Associate

Berkeley Lab • Berkeley, CA

4d • Onsite

About The Position

Lawrence Berkeley National Laboratory has multiple openings for a Scientific Engineering Associate in Berkeley, CA. This role involves performing and supervising nonexempt staff in the development and application of mass spectrometry-related workflows in a high-throughput environment. The associate will apply engineering, scientific, and technical concepts to develop and implement ESI-LC-MS/MS and other mass spectrometry-related workflows for analyzing microbial metabolites and secondary metabolite production. Key responsibilities include troubleshooting LC-MS workflows, developing sample preparation methods, onboarding new instrumentation and protocols, monitoring production metrics, performing data analysis, preparing results for users, managing daily laboratory operations, ensuring safety compliance, and supervising/training technical staff. The role also involves continuous process improvement, collaboration with internal and external partners, contributing to metabolomics infrastructure and LIMS, and contributing to scientific publications.

Requirements

• Bachelor’s Degree in Analytical Chemistry, Engineering, Biochemistry, Bioengineering or a related field and 3 years of experience in the job offered or in a related occupation.
• MS Instrumentation: Operating, maintaining and troubleshooting Thermo Orbitrap ESI-LC-MS/MS mass spectrometry instrumentation such as IQ-X or Exploris mass spectrometers.
• Metabolomics sample processing equipment including UHPLC, SpeedVacs, lyophilizers, centrifuges, N2 generators on a daily basis.
• Onboarding: Onboarding new Thermo Orbitrap MS instrumentation and accessory equipment (N2 generators, UHPLCs, pumps, etc), and implementing them into production in a high-throughput metabolomics environment running over >10k samples/year.
• Method development: Developing and optimizing new ESI-LC-MS/MS methods (MS settings, mobile phases, chromatography, column, etc) to target specific metabolite classes or metabolites such as sugars, lipids, pigment and implementing these in high-throughput metabolomics workflows, as well as incorporating custom data acquisition software workflows (including AcQuireX for iterative MSMS) and similar technologies.
• High-throughput metabolomics production: Preparing and running metabolomics samples using standardized workflows and methods in a high-throughput, production environment (>10k samples/year) using Thermo Orbitrap ESI-LC-MS/MS instrumentation in line with UHPLC, while constantly maintaining instrument uptime, fast turnaround, and high data quality.
• Metabolite extraction: Performing metabolite extraction of thousands of samples/year using a variety of solvents, as well as directly customizing protocols for diverse, complex sample types including soil, bacteria, plant, fungal, environmental, aqueous (including high salt, diverse pH) samples, optimizing solvents (methanol, water, ethyl acetate, chloroform, etc.) and methods.
• Performing day-to-day lab operations in a high-throughput, production metabolomics lab environment with multiple mass spectrometers and sample extraction equipment, including executing workflows, chemical inventory, equipment maintenance, and rigorous lab safety practices involving flammable and toxic materials including storage, use and disposal.
• Documentation: Maintaining precise and detailed laboratory records and documentation.
• Training/mentorship: Training and mentoring others (interns, collaborators, coworkers) in metabolomics sample extraction and solvent handling, usage of processing equipment and running ESILC-MS/MS samples including instrument operation, theory, equipment set-up (mobile phase, etc), maintenance and troubleshooting.

Responsibilities

• Perform and supervise nonexempt staff in the development and application of mass spectrometry-related workflows in a high-throughput environment.
• Apply engineering, scientific, and technical concepts to develop and implement ESI-LC-MS/MS, and other mass spectrometry-related workflows for analyzing microbial metabolites and secondary metabolite production in a high-throughput metabolomics environment.
• Perform, oversee, and expertly troubleshoot all aspects of LC-MS workflows, including sample processing, instrument setup, operation and maintenance, data quality control, software workflows, and coordination with service engineers.
• Develop, optimize, and standardize sample preparation and extraction methods for diverse environmental samples, with particular emphasis on soil.
• Onboard new mass spectrometry instrumentation and protocols and integrate them into high-throughput production workflows.
• Monitor and ensure adherence to production metrics for high-throughput metabolomics workflows.
• Perform both standard and custom mass spectrometry data analysis.
• Prepare results, summaries, and conclusions for JGI users and other collaborators.
• Manage day-to-day laboratory operations, including lab organization and setup, instrument scheduling and prioritization, sample workflows, equipment maintenance, purchasing and inventory of consumables, freezer organization, and waste management.
• Manage and ensure compliance with safety requirements for operating a metabolomics lab.
• Supervise and train technical staff, including undergraduate students, research assistants, providing guidance on LC-MS/MS workflows, data quality control, laboratory procedures, safety practices, and general lab operations.
• Continuously improve and optimize laboratory processes to strengthen metabolomics platform operations, including the development of new internal standard mixtures, analytical methods, and automation protocols.
• Collaborate closely with internal and external partners across JGI groups to customize experimental plans, support cross-team and cross-group R&D projects, and advance user-driven science.
• Contribute to the development, maintenance, and enhancement of metabolomics infrastructure and Laboratory Information Management systems (LIMS).
• Contribute to scientific works, including the preparation and publication of peer-reviewed journal articles.

Benefits

• Salary Range: The full salary range of this position is between $88,560 to $114,828 per year depending upon candidates’ full skills, knowledge, and abilities, including education, certifications, and years of experience.
• Relocation Assistance: This position is not eligible for relocation assistance.

What This Job Offers

• Job Type: Full-time
• Career Level: Entry Level