Scientist II or Senior Scientist, Targeted Proteomics

Role Summary

Scientist II or Senior Scientist, Targeted Proteomics responsible for developing and implementing targeted proteomics workflows to inform drug discovery and development decisions. The role includes collaborating cross-functionally to qualify assays, managing CRO relationships, performing and interpreting MS-based proteomics, and presenting results to internal teams and external collaborators.

Responsibilities

• Develop, optimize, and implement targeted proteomics analysis workflows, including automated enrichment strategies, to deliver precise, accurate, and sensitive protein measurements that inform drug discovery and development decisions.
• Collaborate cross-functionally to implement and qualify assays that drive pipeline decision-making.
• Communicate proactively with project teams and within the proteomics function to coordinate sample availability, align timelines, and ensure timely delivery of high-quality results.
• Manage and oversee activities at contract research organizations (CROs), including assay transfer, qualification, and performance monitoring, ensuring adherence to project specifications, timelines, and data quality standards.
• Perform targeted protein mass spectrometry (MS) assays using state-of-the-art LC-MS systems—including nano-LC and Orbitrap platforms—to determine pharmacodynamic (PD) effects, quantify biomarkers, and qualify assays for clinical studies.
• Prepare samples from a wide variety of biological matrices (cultured cells, tissues, plasma, biofluids) from both human and preclinical species using manual and automated bead-based workflows.
• Perform and interpret quantitative proteomics data analyses using software such as Skyline, MaxQuant, DIANN, and Spectronaut; generate clear, data-driven reports for cross-functional stakeholders.
• Maintain, qualify, and troubleshoot HPLC and MS instrument performance to ensure reliability and reproducibility.
• Present scientific results and strategic recommendations to internal project teams, senior leadership, and external collaborators in a clear, concise, and influential manner.

Qualifications

• Required: PhD in Biochemistry, Biology, Chemistry, or Chemical Biology with a minimum of 2 years of targeted, mass spectrometry–based proteomics experience in industry or startup biotech; or BS/MS with 8+ years of relevant experience.
• Preferred: Familiarity with regulatory filings (e.g., IND) and qualification of MS assays for clinical applications.

Skills

• Broad expertise in targeted proteomics, including development and deployment of highly multiplexed and sensitive PRM or MRM stable isotope–labeled peptide assays using DDA and DIA data.
• Development of immunoaffinity enrichment methods to enhance MS sensitivity.
• Optimization of protein recovery from complex biological matrices (cells, tissues, plasma, biofluids) and various sample formulations (fresh, frozen, FFPE) across preclinical species.
• Operation, maintenance, and troubleshooting of nanoLC and Orbitrap MS instrumentation.
• Quantitative analysis and report generation using Skyline and related proteomics data tools.
• Demonstrated ability to independently analyze, interpret, and clearly communicate targeted proteomics data and conclusions to multidisciplinary teams.
• Proven success collaborating across functional areas and managing CRO relationships to deliver qualified assays that support drug discovery and clinical development.
• Strong organizational, problem-solving, and time-management skills with the ability to prioritize multiple projects to meet TPD drug discovery timelines.
• Excellent written and verbal communication skills, with the ability to convey complex scientific concepts to both technical and non-technical audiences.
• Working knowledge of automated sample processing, including immunoaffinity capture MS assays, is a plus.

Education

• PhD in Biochemistry, Biology, Chemistry, or Chemical Biology with equivalent industry experience (2 years post-PhD) or BS/MS with 8+ years of relevant proteomics experience.