Research Scientist III / Senior Research Scientist

Sapient • San Diego, CA

Associate Posted April 3, 2026 Job link

Responsibilities

On the Associate team at Sapient in San Diego, you'll prepare and process diverse protein samples using techniques such as chromatography, nanoparticle enrichment, and solid phase extraction, and perform discovery and targeted proteomics via DDA/DIA and PRM mass spectrometry. You will analyze proteomics data using tools like Spectronaut, Skyline, and MSFragger; independently operate, troubleshoot, and maintain key instruments; develop and document new laboratory methods and maintain a clear ELN. You’ll also review and QC analytical data under GLP/GCP, support specimen and consumables management, maintain a safe and efficient lab environment, collaborate effectively across the organization, and reliably learn and execute complex new techniques.

Commitments

This is a full-time, on-site position in Sorrento Valley, San Diego, with a salary range of $85,000–$115,000 depending on qualifications and experience, and includes other duties as assigned.

Responsibilities

Prepares samples using techniques such as size exclusion chromatography, nanoparticle enrichment and solid phase extraction.
Prepares protein samples from a wide range of specimens (e.g., cells, tissue, biofluids, recombinant proteins) for discovery and targeted proteomics analysis
Conducts global proteome profiling by data-dependent (DDA) and data-independent (DIA) acquisition mass spectrometry, as well as experiments for post-translational modifications (e.g., phosphorylation, acetylation).
Conducts relative and absolute quantitative analysis using Parallel Reaction Monitoring (PRM) mass spectrometry.
Uses key software tools for proteomics data analysis (e.g., Spectronaut, Skyline, MSFragger)
Independently operates laboratory equipment and performs basic troubleshooting and routine maintenance on instruments (e.g., timsTOF Pro 2, Thermo Stellar)
Assists with developing new methods for testing in the laboratory and maintains detailed records of development, interpretation and results.
Maintains clear and organized electronic laboratory notebook (ELN), documenting protocols, reagent preparation, and results of all experiments performed in real time.
Reviews and QCs analytical data using manual and automated pipelines and uses analytical abilities to make decisions regarding the accuracy of results.
Performs all responsibilities in adherence with regulatory principles and best laboratory practices such as GLP/GCP.
Establishes excellent working relationships with key collaborators throughout the organization and communicates effectively through appropriate channels and tools.
Demonstrates the ability to complete projects in a communicative and timely manner under regulatory guidance.
Maintains safe and efficient procedures in the laboratory.
Supports the organization, tracking, and storing of specimens.
Supports management of lab consumables, including ordering, receiving, and storage of consumables.
Demonstrates the ability to learn complex tasks with instruction and to apply this to perform a variety of new techniques.

Not Met Priorities

What still needs stronger evidence

Requirements

As an RSIII/SRS, you will be responsible for performing laboratory experiments such as the preparation of clinical and biological samples for global/targeted proteomics analyses using medium to high throughput liquid chromatography mass spectrometry instrumentation.
Experience with size exclusion chromatography, nanoparticle and other proteomics enrichment preparations, BCA and SPE techniques.
Familiarity with mass spectrometry techniques (preferably untargeted LC-MS, however targeted LC-MS is also favorable) and working in a BSL2/BSL2+ environment.
Experience with custom data workflows and data analysis required (i.e., Skyline, Specronaut, mzmine)
Prepares samples using techniques such as size exclusion chromatography, nanoparticle enrichment and solid phase extraction.
Prepares protein samples from a wide range of specimens (e.g., cells, tissue, biofluids, recombinant proteins) for discovery and targeted proteomics analysis
Conducts global proteome profiling by data-dependent (DDA) and data-independent (DIA) acquisition mass spectrometry, as well as experiments for post-translational modifications (e.g., phosphorylation, acetylation).
Uses key software tools for proteomics data analysis (e.g., Spectronaut, Skyline, MSFragger)
Independently operates laboratory equipment and performs basic troubleshooting and routine maintenance on instruments (e.g., timsTOF Pro 2, Thermo Stellar)
Assists with developing new methods for testing in the laboratory and maintains detailed records of development, interpretation and results.
Maintains clear and organized electronic laboratory notebook (ELN), documenting protocols, reagent preparation, and results of all experiments performed in real time.
Reviews and QCs analytical data using manual and automated pipelines and uses analytical abilities to make decisions regarding the accuracy of results.

Preferred Skills

Experience with size exclusion chromatography, nanoparticle and other proteomics enrichment preparations, BCA and SPE techniques.
Familiarity with mass spectrometry techniques (preferably untargeted LC-MS, however targeted LC-MS is also favorable) and working in a BSL2/BSL2+ environment.
Experience with custom data workflows and data analysis required (i.e., Skyline, Specronaut, mzmine)

Education

(Not required) – Bachelor's degree in biology, Biochemistry, Chemistry, or a related Life Science field and 3+ years of related work experience or a master’s degree with 1 year of related work experience.

About Us Sapient is an early-stage fee for service, contract research organization in San Diego, CA. Our focus is on accelerating drug development and transforming personalized medicine for our pharma and biotech clients. We are an agile, highly collaborative team of passionate scientists, committed to making innovations with scientific rigor, and executing in a timely manner in accordance with key regulatory standards. Combining state-of-the-art mass spectrometry technology with advanced biocomputational services and multifaceted human health data, we enable biomarker discovery at unprecedented speed and scale to provide a deeper understanding of human biology and effectively align biological targets, patients, and drug therapies in support of our clients. About the Role We are in search of a Research Scientist II|/Senior Research Scientist with expertise primarily in proteomics workflows for complex matrices (e.g., biosamples) to join our interdisciplinary bioanalytical team here at Sapient. As an RSIII/SRS, you will be responsible for performing laboratory experiments such as the preparation of clinical and biological samples for global/targeted proteomics analyses using medium to high throughput liquid chromatography mass spectrometry instrumentation. What we’re looking for For RSIII/SRS :
Experience with size exclusion chromatography, nanoparticle and other proteomics enrichment preparations, BCA and SPE techniques.
Familiarity with mass spectrometry techniques (preferably untargeted LC-MS, however targeted LC-MS is also favorable) and working in a BSL2/BSL2+ environment.
Experience with custom data workflows and data analysis required (i.e., Skyline, Specronaut, mzmine)
Bachelor's degree in biology, Biochemistry, Chemistry, or a related Life Science field and 3+ years of related work experience or a master’s degree with 1 year of related work experience. Responsibilities/Skills Technical Duties
Prepares samples using techniques such as size exclusion chromatography, nanoparticle enrichment and solid phase extraction.
Prepares protein samples from a wide range of specimens (e.g., cells, tissue, biofluids, recombinant proteins) for discovery and targeted proteomics analysis
Conducts global proteome profiling by data-dependent (DDA) and data-independent (DIA) acquisition mass spectrometry, as well as experiments for post-translational modifications (e.g., phosphorylation, acetylation).
Conducts relative and absolute quantitative analysis using Parallel Reaction Monitoring (PRM) mass spectrometry.
Uses key software tools for proteomics data analysis (e.g., Spectronaut, Skyline, MSFragger)
Independently operates laboratory equipment and performs basic troubleshooting and routine maintenance on instruments (e.g., timsTOF Pro 2, Thermo Stellar)
Assists with developing new methods for testing in the laboratory and maintains detailed records of development, interpretation and results.
Maintains clear and organized electronic laboratory notebook (ELN), documenting protocols, reagent preparation, and results of all experiments performed in real time.
Reviews and QCs analytical data using manual and automated pipelines and uses analytical abilities to make decisions regarding the accuracy of results.
Performs all responsibilities in adherence with regulatory principles and best laboratory practices such as GLP/GCP. General Duties
Establishes excellent working relationships with key collaborators throughout the organization and communicates effectively through appropriate channels and tools.
Demonstrates the ability to complete projects in a communicative and timely manner under regulatory guidance.
Maintains safe and efficient procedures in the laboratory.
Supports the organization, tracking, and storing of specimens.
Supports management of lab consumables, including ordering, receiving, and storage of consumables.
Demonstrates the ability to learn complex tasks with instruction and to apply this to perform a variety of new techniques.
Other duties as assigned Position Location - San Diego, California (Sorrento Valley) Position Type - Full-time, On-site Compensation – $85,000 – 115,000 final compensations will be based on qualification and experience)