Analytical Development Research Scientist, Cell and Gene Therapy Proteomics

Summary: Vertex Pharmaceuticals is seeking a research scientist to join the analytical development, cell and gene therapy team. The primary focus of this role will be on proteomics analysis for stem cell differentiation and leveraging multi-omics tools to achieve a deeper understanding of cell therapy products. Responsibilities: - Provide hands-on support for mass spectrometry-based proteomics characterization and perform biological pathway & bioinformatics analysis. Mass Spectrometry analysis includes but not limited to tandem-mass-tag (TMT) and label-free quantification, data-dependent and independent acquisitions, sub-cellular fractionations, Post translational modification (PTM) enrichments, etc - Conduct proteomics experiments on different cell types including but not limited to stem cells, differentiated cells, different cellular compartments, and understand post translational modification profiling at proteome level through different sample preparation and mass spectrometry fragmentation techniques - Perform proteomics data analysis using relevant software, including protein ID, quantitation, statistical and pathway analysis - Integrate proteomics data with other omics datasets (e.g., transcriptomics, metabolomics) to provide a comprehensive understanding of cell therapy products. Utilize bioinformatics tools and statistical methods to analyze complex datasets from epigenetics and multi-omics studies - Provide expertise in experimental design, data analysis, assay trouble shooting, technical report writing, and presentations. Generate actionable insights to guide process development, product optimization, and regulatory submissions - Interface with external vendors and partners, manage external sample testing, review and analyze data as needed - Author analytical method, qualification, and validation reports; author data summary reports - Maintain proper documentation of experimental results and data interpretations - Ensure data quality and maintain data integrity of analytical results to support decision making - Collaborate with research and process development teams to develop fit-for-purpose analytical characterization methods for target optimization, product characterization, and product investigations Required Qualifications: - Extensive hands-on experience in liquid chromatography-mass spectrometry-based proteomics is required - Strong hands-on experience on LC-MS based proteomics analysis and Orbitrap mass spectrometers is required - Strong hands-on experience with advanced proteomics sample preparation techniques for protein isolation from cells, sub-cellular fractionation, histone extraction, immuno- or chemical affinity purification is required - Strong hands-on experience with label free and TMT based multiplex quantification is required - Strong hands-on experience with proteomics data analysis and multi-omics data integration with commercially available software platforms is required - Demonstrated capabilities to independently digest and formulate experimental conclusions by referencing orthogonal analytical results - Ability to use information gained from experiments to inform method and program decisions - Skilled in efficient study design and demonstrated expertise in writing SOPs, analytical protocols, and reports - Ability to multi-task as necessary, managing competing priorities, and advancing multiple projects within required timelines - Demonstrated ability to work cross-functionally to drive communication, strong track record in cross-team collaboration - Strong oral and written communication skills - Ph.D. (or equivalent degree) and 0-3 years of relevant post-doctoral employment experience, or - Masters Degree (or equivalent degree) and 3+ years of relevant employment experience, or - Bachelors Degree (or equivalent degree) and 6+ years of relevant employment experience Preferred Qualifications: - A deep understanding of stem cell biology is strongly preferred - Hands on experiences on stem cell culturing, handling, and stem cell differentiation is a plus - Experiences with both data dependent acquisition and data independent acquisition are preferred - Experiences with single cell proteomics is preferred Required Skills: LC-MS based proteomics analysis, Orbitrap mass spectrometers, Stem cell biology, Stem cell culturing, Stem cell differentiation, Proteomics sample preparation, Protein isolation, Sub-cellular fractionation, Histone extraction, Immunoaffinity purification, Chemical affinity purification, Label free quantification, TMT based multiplex quantification, Proteomics data analysis, Multi-omics data integration, Data dependent acquisition, Data independent acquisition, Single cell proteomics, Experimental design, SOP writing, Analytical protocol writing, Analytical report writing, Cross-team collaboration Benefits: Medical, dental and vision benefits, Generous paid time off (including a week-long company shutdown in the Summer and the Winter), Educational assistance programs including student loan repayment, A generous commuting subsidy, Matching charitable donations, 401(k)