Mass Spectrometry Scientist
FYR, Missoula, MT, United States
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 is 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 abilitiesHighly 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
#J-18808-Ljbffr
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 is 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 abilitiesHighly 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
#J-18808-Ljbffr