Research Scientist, Proteomics & Mass Spectrometry (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

Job Description

General Summary

Vertex Pharmaceuticals is seeking a Contract Research Scientist, Proteomics & Mass Spectrometry to join the Chemical Biology group. This on-site laboratory role supports mass spectrometry–based research in proteomics, and targeted quantification of small molecules and lipids. The position supports research activities including target discovery, screening validation, biomarker research, and mechanism-of-action investigations within Chemical Biology and across functions in Boston Research.

Key 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, analyte enrichment or depletion, labeling, immunoprecipitation, enzymatic digestion, cleanup, and extraction. This includes use of liquid-handling instrumentation.
• Generate and operate LC-MS assays, including DIA, DDA, PRM, and related workflows.
• Operate, maintain, calibrate, and perform first-line troubleshooting of LC-MS systems, including Thermo and Bruker platforms.
• Monitor defined instrument-performance and assay-quality metrics; identify and elevate performance trends or technical issues according to laboratory procedures.
• Process mass spectrometry data using established analysis workflows and software; complete routine data-quality review, visualization, reporting, and data upload or storage.
• Maintain laboratory supplies, reagents, consumables, and work areas needed to support scheduled experiments and instrument operation.
• Coordinate in a matrix team on experiment priorities and schedules, shared lab work, status and technical issues.
• Communicate experimental results and technical updates through ELNs, presentations and team discussions.

Education and Experience

• PhD with hands-on relevant experience in analytical chemistry, biochemistry, chemical biology or related field. Bachelors or MSc with equivalent years of relevant education, technical training, and directly applicable laboratory experience will be considered.
• 5+ years of hands-on experience with three or more of the following: protein or peptide sample preparation, proteomics, chemoproteomics, analytical chemistry, LC-MS lipid analysis, or small-molecule mass spectrometry.
• Experience following laboratory procedures for biological sample processing, including three or more of cell culture, cloning, proximity labeling, immunoprecipitation, automation, fractionation, digestion.
• 5+ years experience operating LC-MS instrumentation or directly supporting LC-MS experimental workflows including instrument maintenance, calibration, performance monitoring, and troubleshooting.
• Experience with one or more mass-spectrometry data-analysis platforms, such as Spectronaut, Skyline, Proteome Discoverer, MsFragger, or comparable software.

Pay Range

$60-$63/HR