Senior Scientist, Proteomics

Company Summary:

ProFound Therapeutics is discovering proteins hidden within the expanded human proteome to uncover novel drugs and drug targets, producing first-in-class medicines for a multitude of diseases. The company’s ProFoundry™ Platform uses state-of-the-art protein detection technologies to systematically identify and validate proteins and dissect their therapeutic potential. The result is an ever-expanding database of tens of thousands of novel proteins, including their connectivity, functionality, and roles in health and disease. ProFound Therapeutics was founded in 2020 by Flagship Pioneering. For more information, please visit www.profoundtx.com.

Job Description:

We are looking for a highly skilled and driven Senior Scientist specializing in Proteomics, with extensive experience in Mass Spectrometry, to join our dynamic and expanding Profound Proteomics team. The ideal candidate will possess in-depth expertise in high-resolution mass spectrometry, membrane protein enrichment and analysis, immunoprecipitation-mass spectrometry, pathway analysis, targeted proteomics, and laboratory automation.

This position presents a unique opportunity to engage in groundbreaking research on the “expanded proteome” exploring uncharted territories in protein identification, characterization, and understanding.

Key Responsibilities:

• Develop and implement innovative proteomics strategies specifically targeting the dark proteome
• Lead and execute proteomic projects with a focus on high-resolution mass spectrometry analysis and discovery and validation of novel proteins
• Design and optimize IP-MS workflows to investigate protein interactions and elucidate pathways
• Create and optimize high-sensitivity assays for analysis in cellular and tissue samples
• Conduct dedicated target validation workflows (e.g., IP-MS, PRM, bead- and antibody-based enrichment, PTM analysis)
• Operate and maintain Proteomics laboratory equipment
• Interpret and present complex data to both scientific and non-scientific audiences
• Collaborate with cross-functional teams to integrate proteomics data with other omics technologies
• Streamline and optimize current proteomic workflows while exploring and developing new methodologies
• Excellent communication and interpersonal skills, with the ability to work effectively in a collaborative team environment

Qualifications:

• Ph.D. in Biochemistry, Molecular Biology, Analytical Chemistry, or a related field with a strong emphasis on proteomics with 5+ years of relevant postdoctoral training or industry experience strongly preferred.
• Proven expertise with high-resolution mass spectrometry (e.g., Orbitrap, Q-TOF).
• Experience in membrane protein analysis and IP-MS techniques
• Solid background in proteomics sample preparation, peptide analysis and quantification workflows
• Experience in automated workflows (including PTMs analysis) to process samples in 96-well plates 
• Experience with high resolution mass spectrometers (mostly Q-TOF and Orbitrap), DIA and PRM acquisitions, and major software packages (such as Biognosys, Byos, Fragmatics, Skyline)
• Experience in de-novo peptide sequencing and immunopeptideomics is a plus
• Demonstrated ability to independently design and troubleshoot experiments
• Excellent analytical skills with a strong attention to detail
• Strong track record of scientific publications in reputable journals

Values and Behaviors

We are seeking individuals with an entrepreneurial spirit, strong communication skills, and comfort working in and contributing to a dynamic and cross-functional team environment. The level of the role will be commensurate with the education and years of experience of the identified candidate.

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

About Flagship

Flagship Pioneering is a biotechnology company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health