Senior Scientist I, Proteomics Platform

The Role:

Generate: Biomedicines is seeking an experienced and highly motivated Senior Scientist, Proteomics Platform to join our team at the interface of proteomics, molecular biology, ML, and biopharmaceutical discovery.

This role will be central to reimagining and building proteomics capabilities for large-scale data generation and high-throughput screening, using a rapid prototyping mindset to construct tools, workflows, and capabilities across the full proteomics pipeline.

The ideal candidate will bring deep technical expertise spanning the full proteomics workflow, from sample preparation and LC-MS/MS method development through data processing, interpretation, and cross-study analysis. This person will have a strong track record of building tools, workflows, and analytical pipelines around proteomics technologies, and will be excited to work closely with Automation, Machine Learning, and Data Science teams to develop new experimental and computational capabilities.

This role is well suited for someone who can execute at a high technical level while also rethinking proteomics systems end-to-end: designing fit-for-purpose workflows, rapidly prototyping new capabilities, and translating emerging ideas into differentiated experimental approaches that accelerate discovery.

Here's how you will contribute:

• Design, execute, and optimize end-to-end proteomics workflows spanning sample preparation, LC-MS/MS data acquisition, data processing, and multi-experiment analysis in support of discovery and screening efforts.
• Build, prototype, and refine proteomics-centered tools, workflows, and analysis pipelines that enable rapid generation of high-quality data and scalable downstream interpretation.
• Construct tools and workflows for customizing DDA, DIA, and PRM acquisition methods, with clear understanding of the tradeoffs between these approaches and their fit-for-purpose applications.
• Partner closely with machine learning, data science, automation, and software teams to define requirements for proteomics data structure, quality control, metadata capture, and analytical capabilities.
• Lead the development of proteomics data processing, interpretation, and comparison approaches across experiments, campaigns, and datasets.
• Develop and adapt sample preparation methods for diverse proteomics applications, including workflows involving SP3, S-Trap, StageTips, immunoprecipitation, low-input samples, and related techniques.
• Operate, troubleshoot, and improve advanced proteomics workflows on state-of-the-art mass spectrometry platforms, with emphasis on Bruker timsTOF and Thermo Orbitrap instruments.
• Contribute to the design of platform capabilities to enable differentiated and proprietary approaches.
• Work across molecular biology, protein sciences, and drug discovery teams to identify opportunities where proteomics can unlock new experimental strategies, mechanistic insight, or screening modalities.
• Present findings clearly to multidisciplinary stakeholders and help shape experimental strategy, platform direction, and technical decision-making.

The Ideal Candidate will have:

• PhD in Analytical Chemistry, Proteomics, Biochemistry, Molecular Biology, or a related field, with 4+ years relevant postdoctoral and/or industry experience; or MS with 8+ years industry experience.
• Significant hands-on experience establishing and advancing mass spectrometry-based proteomics platforms, preferably in a biotech, pharmaceutical, or applied research environment.
• Deep expertise across the full proteomics workflow, including sample preparation, chromatographic separation, mass spectrometry data acquisition, data processing, and downstream comparative analysis across experiments or datasets.
• Strong experience designing, building, and improving proteomics workflows, analytical methods, or data pipelines rather than solely executing established assays.
• Deep expertise with modern proteomics instrumentation, especially Bruker timsTOF and Thermo Orbitrap platforms.
• Strong understanding of proteomics acquisition methods, including DDA, DIA, and PRM, and the ability to select, adapt, and optimize these approaches based on experimental goals.
• Extensive experience with liquid chromatography for proteomics, including nano-ESI workflows, direct inject, and trap-and-elute.
• Strong proficiency in proteomics data analysis tools, including PEAKS, Spectronaut, Skyline, Protein Metrics, and/or custom or open-source analysis workflows.
• Extensive knowledge of proteomics sample preparation techniques, including SP3, S-Trap, StageTips, immunoprecipitation, single-cell proteomics, and low-input proteomics, with demonstrated experience developing and applying workflows across diverse sample types including purified proteins, cell lysates, tissues, and in vivo samples.
• Demonstrated programming and computational problem-solving ability for scientific data analysis, workflow development, pipeline construction, and/or automation.
• Strong experimental design, troubleshooting, and systems-thinking skills, with the ability to understand and improve proteomics workflows end to end.
• Excellent communication and collaboration skills, with the ability to work effectively across proteomics, molecular biology, automation, machine learning, and data science teams.

Preferred Qualifications

• Experience building or scaling proteomics data processing and analysis pipelines.
• Experience working closely with machine learning, data science, or software teams to structure experimental data for downstream modeling and cross-study analysis.
• Experience rapidly prototyping new proteomics capabilities in support of discovery goals.
• Experience developing or improving proteomics sample preparation workflows for challenging, low-input, or high-throughput applications.
• Experience with protein purification approaches using magnetic beads, resins, and high-throughput automation.
• Working knowledge of protein production, DNA assembly, and protein purification strategies.
• Experience applying proteomics in the context of biopharmaceutical or therapeutic protein discovery.
• Experience using Benchling to support experimental design, sample and sequence tracking, and cross-functional collaboration in molecular biology and protein science workflows.
• Familiarity with highly collaborative, matrixed research environments where analytical science, data science, and discovery biology are tightly integrated.

What You’ll Bring

• Scientific rigor and deep technical judgment across the full proteomics workflow.
• A builder’s mindset with enthusiasm for creating tools, workflows, and capabilities around proteomics technologies.
• A fast-prototyping mentality and comfort working in environments where new capabilities are developed iteratively to answer important questions quickly.
• The ability to connect experimental design, data generation, and computational interpretation into a coherent end-to-end system.
• Curiosity about biological mechanisms and the role of proteomics in therapeutic discovery.
• A collaborative spirit and a desire to contribute to an ambitious, interdisciplinary team.

About Generate Biomedicines

We are a clinical-stage generative biology company pioneering the AI revolution in drug design and development. We are advancing a new approach to drug creation—one grounded in the ability to design proteins with defined biological intent. By integrating machine learning with large-scale experimentation, this approach aims to reduce the uncertainty, time, and cost associated with developing protein-based medicines.

Founded in 2018, we are advancing a growing pipeline of clinical and preclinical programs across multiple disease areas and protein modalities. By unifying computational design and clinical development within a single operating model, we translate this approach into clinical-stage programs and are leading a shift from traditional drug discovery toward systematic drug generation.

At Generate:Biomedicines, we collaborate across disciplines in new ways to invent and innovate. We bring diverse perspectives to a shared goal of delivering better medicines to patients in need, faster, guided by our values and leadership behaviors.

Generate:Biomedicines is committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.

Recruitment & Staffing Agencies: Generate:Biomedicines does not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to Generate:Biomedicines or its employees is strictly prohibited unless contacted directly by the Company’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of Generate:Biomedicines and the Company will not owe any referral or other fees with respect thereto.

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