Mass Spectrometry Scientist

At Two Bear Capital we believe in partnering with our companies to build the best teams possible. We look forward to working with you and FYR Bio for their new Mass Spectrometry Scientist to lead and operationalize their proteomics infrastructure.

** please note that this position in based on-site in Missoula, Montana **

About FYR Bio

At FYR Bio, we are driven by a vision to unlock biological complexity to illuminate human health, and our mission is to bring the promise of EV-based precision medicine to patient care. This position will play a key role in establishing and scaling FYR Bio's proteomics platform and will directly contribute to both internal discovery programs and the delivery of high-quality data for our biotechnology and pharmaceutical partners.

We are seeking an experienced Mass Spectrometry Scientist to lead and operationalize our proteomics infrastructure. This role offers a unique opportunity to build and scale foundational proteomics capabilities that directly contribute to our vision, bridging cutting-edge technology with real-world clinical impact.

Position Overview

We are seeking a highly experienced Mass Spectrometry Scientist with deep expertise in LC-MS/MS proteomics to build, establish, and scale mass spectrometry infrastructure at FYR.

This role will be responsible for developing and managing proteomic workflows, maintaining high-resolution mass spectrometry instrumentation, processing samples for internal and client-driven projects, and ensuring compliance for studies associated with pharmaceutical R&D and clinical trials.

The position also includes operational leadership responsibilities such as budgeting, project planning, vendor coordination, and supervision of laboratory personnel.

Key Responsibilities

Proteomics & Mass Spectrometry Operations

• Develop, implement, and optimize LC-MS/MS proteomic workflows for both discovery and quantitative studies
• Operate and maintain high-resolution MS instrumentation, including platforms such as the Thermo Fisher Orbitrap Astral or Bruker timsTOF HT
• Oversee sample preparation workflows including protein extraction, digestion, peptide cleanup, and quality control
• Manage large-scale sample processing across multiple internal and external projects
• Monitor and maintain instrument performance through calibration, preventative maintenance, and troubleshooting
• Lead installation, qualification, and validation of new mass spectrometry instrumentation

Data Analysis & Proteomics Pipeline Development

• Oversee proteomics data processing and analysis pipelines including peptide/protein identification, quantification, normalization, and QC
• Implement and maintain reproducible computational workflows for proteomic data analysis
• Support both data-dependent acquisition (DDA) and data-independent acquisition (DIA) proteomics workflows
• Manage spectral library generation, database searching, and statistical validation of results
• Collaborate with bioinformatics teams to enable downstream analysis and data integration
• Ensure robust data management, storage, and traceability across projects

Clinical Compliance & Quality Systems

• Ensure workflows meet appropriate compliance standards for studies supporting pharmaceutical and clinical trial programs
• Maintain documentation and SOPs consistent with GLP, GCP, and 21 CFR Part 11 requirements where applicable
• Establish and manage sample tracking, chain-of-custody procedures, and audit-ready documentation
• Support regulatory audits and client quality reviews
• Participate in method development, validation, and quality control processes

Laboratory Operations & Infastructure

• Build MS functionalities and capacity that support our strategic plan and once established, oversee day-to-day operations of the mass spectrometry laboratory
• Develop and manage operational budgets including instrumentation service contracts, reagents, and consumables
• Coordinate with vendors for installation, maintenance, and technical support
• Contribute to laboratory design and infrastructure planning for MS instrumentation (power, gas supply, vibration control, etc.)
• Implement laboratory information management systems (LIMS) and data tracking workflows

Project & Team Leadership

• Plan and prioritize MS workflows across multiple internal R&D and client-facing projects
• Provide project scoping support for new client engagements and collaborations
• Hire, train, and supervise laboratory staff involved in proteomics workflows
• Communicate project progress, risks, and timelines to internal teams and external partners
• Collaborate closely with multidisciplinary teams including bioinformatics, molecular biology, and clinical research groups

Required Qualifications

• PhD in Analytical Chemistry, Proteomics, Biochemistry, or related field (or MS with extensive relevant experience)
• 5 years of hands-on experience in LC-MS/MS proteomics workflows
• Direct experience operating and maintaining high-resolution MS platforms such as Orbitrap or timsTOF systems
• Strong expertise in quantitative proteomics, including DIA or other high-throughput workflows
• Demonstrated ability to manage complex experimental pipelines involving large sample sets
• Working knowledge of compliance requirements for clinical or pharmaceutical research
• Experience troubleshooting MS instrumentation and optimizing experimental workflows
• Strong organizational and communication skills
• Ability to work collaboratively within a multidisciplinary scientific team

Preferred Qualifications

• Experience establishing or scaling a proteomics laboratory or MS core facility
• Expertise in DIA-based proteomics workflows such as Astral DIA or diaPASEF
• Experience with proteomics software tools including Proteome Discoverer, MaxQuant, Spectronaut, DIA-NN, FragPipe, or Skyline
• Familiarity with automated sample preparation platforms and high-throughput laboratory workflows
• Experience implementing or managing LIMS systems
• Experience supporting pharmaceutical or CRO client services
• Experience developing spectral libraries and advanced quantitative proteomic pipelines
• Experience supervising laboratory staff or leading technical teams
• Familiarity with data infrastructure such as HPC or cloud-based data processing environments

Personal Attributes

• Strong work ethic and commitment to high-quality scientific work
• Excellent problem-solving and troubleshooting abilities
• Highly organized and detail-oriented
• Ability to manage multiple projects and priorities simultaneously
• Effective communicator capable of interacting with both technical and non-technical stakeholders
• Collaborative team player with the ability to operate in a fast-paced environment