On-Site Proteomics & Mass Spectrometry Scientist (Contract)

Vertex Pharmaceuticals LLC; Boston (MA); On-site; USD 83,000 - 87,000; Full time

Job summary

Vertex Pharmaceuticals LLC in Boston seeks a Contract Research Scientist specializing in Proteomics & Mass Spectrometry to join the Chemical Biology group. The role supports MS-based proteomics, quantification of small molecules, and biomarker research in an on-site laboratory.

You will execute LC-MS workflows, prepare samples, operate DIA/DDA/PRM assays, maintain instruments, review data, and collaborate across functions in a fast-paced environment.

Qualifications

• PhD with hands-on experience in analytical chemistry, biochemistry, chemical biology or related field.
• 5+ years hands-on experience with proteomics, chemoproteomics, LC-MS lipid analysis, or small-molecule MS.
• Experience following lab procedures for biological sample processing including cell culture, cloning, proximity labeling, immunoprecipitation, automation, fractionation, digestion.
• 5+ years operating LC-MS instrumentation and supporting LC-MS workflows including maintenance and troubleshooting.
• Experience with data-analysis platforms such as Spectronaut, Skyline, Proteome Discoverer, MsFragger.

Responsibilities

• Execute established sample-preparation and LC-MS workflows for proteomic, chemoproteomic, lipid, and small-molecule experiments.
• Prepare samples for mass spectrometry, including cell lysis, protein extraction, enrichment or depletion, labeling, immunoprecipitation, digestion, cleanup, and extraction using liquid-handling equipment.
• Generate and operate LC-MS assays, including DIA, DDA, PRM, and related workflows.
• Operate, maintain, calibrate, and troubleshoot LC-MS systems on Thermo and Bruker platforms.
• Monitor instrument-performance and assay-quality metrics; escalate issues per procedures.
• Process MS data with established workflows; perform data-quality review, visualization, and reporting.
• Maintain laboratory supplies, reagents, and workspace for experiments and instrument operation.
• Coordinate in a matrix team on experiment priorities, shared lab work, and scheduling.
• Communicate results and updates through ELNs, presentations and discussions.

Skills

Proteomics

Mass spectrometry

Chemoproteomics

Biochemistry

Education

PhD in Analytical Chemistry, Biochemistry, Chemical Biology or related field

Bachelor's or MSc with equivalent years of relevant education

Tools

Spectronaut

Skyline

Proteome Discoverer

MsFragger

LC-MS instrumentation

Job description

Vertex Pharmaceuticals LLC in Boston seeks a Contract Research Scientist specializing in Proteomics & Mass Spectrometry to join the Chemical Biology group. The role supports MS-based proteomics, quantification of small molecules, and biomarker research in an on-site laboratory.

You will execute LC-MS workflows, prepare samples, operate DIA/DDA/PRM assays, maintain instruments, review data, and collaborate across functions in a fast-paced environment.