Position Summary

The Proteomics Research Scientist will be responsible for designing, executing, and optimizing proteomics-based workflows with a primary focus on high-resolution mass spectrometry using Orbitrap platforms. This role involves developing quantitative and qualitative proteomic assays, biomarker discovery pipelines, and supporting translational research and clinical diagnostic applications. The scientist will collaborate cross-functionally with R&D, bioinformatics, quality assurance, and clinical operations teams to advance proteomics initiatives from research through clinical validation.

Key Responsibilities

Experimental Design & Execution

Develop, optimize, and implement targeted proteomics analysis workflows, including automated enrichment strategies, for precise, accurate, and sensitive protein measurements using stable isotope dilution and label-free mass spectrometry
Coordinate with project teams to identify targeted proteomics assay requirements, timing, samples and deliverables
Perform targeted protein MS assays using state-of-the-art LC-MS systems; including Horizon-LC, Orbitrap MS platforms to determine protein concentrations in various human sample matrices
Prepare samples from a wide variety of biological matrices (cultured cells, tissues, plasma, biofluids) from human and preclinical species using manual and automated bead-based workflows
Perform data analysis utilizing a range of proteomics software (Skyline, MaxQuant, DIANN, Spectronaut)
Maintain and qualify HPLC and MS instrument performance
Coordinate with multiple project teams to deploy the developed proteomics assay into manufacturing line, and ensure the workflow is optimized.

Instrumentation & Technology Management

Operate, maintain, and troubleshoot Orbitrap mass spectrometers (e.g., Exploris, Fusion, Q-Exactive series) and associated nanoLC systems.
Perform routine calibration, performance checks, and preventive maintenance.
Work with vendors to implement new upgrades, applications, and service support.

Data Analysis & Bioinformatics

Process and interpret raw mass spectrometry data using specialized software (e.g., Proteome Discoverer, MaxQuant, Skyline, Spectronaut).
Integrate proteomics datasets with genomics, metabolomics, or other omics data for multi-dimensional insights.
Collaborate with bioinformatics teams to refine pipelines, perform statistical analyses, and generate clinically relevant reports.

Research & Development

Lead biomarker discovery projects and translate findings into clinical assays.
Explore proteomics applications for precision medicine, oncology, immunology, neurodegenerative, metabolic, and cardiovascular diseases.
Stay current with literature, emerging technologies, and regulatory trends in proteomics and clinical mass spectrometry.

QualificationsEducation

PhD in Biochemistry, Biology, Chemistry, Chemical Biology with minimally 5+ years of experience in targeted mass spectrometry-based proteomics in industry or startup biotech setting or MS with 10+ years of experience
Broad experience in targeted MS is required:
Hands on experiences on targeted MS method development and execution, including highly multiplexed and sensitive PRM stable isotope labeled peptide assays using DDA and DIA data
Hands on experiences in operating, maintaining and troubleshooting nano LC and Orbitrap MS instruments
Hands-on experience in sample preparation method development and optimization from various matrices (cells, tissues, plasma, biofluids)
Demonstrated ability to independently analyze, and interpret targeted proteomics data, and communicate effectively in a fast paced, team-oriented environment
Experiences in expression proteomics and chemoproteomics are highly desirable:
Demonstrated ability to develop methods and lead mechanism of action mass spectrometry studies
Develop and optimize mass spectrometry screening assays based on project needs
Experience with sample preparation from primary cells is a plus
Motivated problem solver with attention to details, great organization skills and time management, and ability to multitask efficiently to meet drug discovery timelines, team player

Work Environment & Physical Demands

Laboratory-based role with routine handling of biological and chemical samples.
Requires extended periods at mass spectrometry instruments and computational workstations.
Occasional weekend/evening work for long LC-MS runs or instrument troubleshooting.

Job Type: Full-time

Pay: $180,000.00 - $250,000.00 per year

Benefits:

401(k) matching
Dental insurance
Health insurance
Vision insurance

Work Location: In person

Vibrant America

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Proteomics Research Scientist