Empress: Proteomics Co-Op

Flagship Pioneering•Cambridge, MA

About The Position

Empress is pioneering mechanistic intelligence for drug discovery — helping R&D teams understand what their molecules are doing, what is driving activity, what liabilities may emerge, and which candidates are best positioned to advance. By integrating multi-omics, chemoproteomics, proteomics, transcriptomics, computational inference, knowledge graphs, and CRISPR-based functional validation, Empress turns biological complexity into clearer development decisions. Our platform gives discovery teams access to capabilities that would otherwise require years, specialized infrastructure, and rare cross-functional expertise to build internally. Empress is a privately held biotech conceived by Flagship Pioneering, which brings the courage, long-term vision, and resources needed to realize unreasonable results. The Role We're looking for a Co-op to join our Proteomics team and contribute to the development of Empress's Integromyx and Perturb-seq platforms. You'll get hands-on experience across the full mass spectrometry-based proteomics workflows, from cell culture and sample preparation through LC-MS/MS acquisition on Orbitrap systems, including exposure to chemoproteomics experiments that sit at the intersection of chemistry and biology. You'll work as part of a cross-functional team where your contributions matter from day one. We're looking for someone who is curious, detail-oriented, and eager to develop their skills alongside a team building something new.

Requirements

Currently enrolled in a B.S. or M.S. program in Chemistry, Chemical Biology, Biochemistry, or a related field
Coursework or hands-on laboratory experience in chemical biology, liquid chromatography, or mass spectrometry

Nice To Haves

Familiarity with analytical techniques with a focus on mass spectrometry, especially Thermo Fisher instrumentation
Experience with liquid chromatography sample preparation and purification
Familiarity with R, Python, or strong interest in learning informatics tools
Interest in lab automation instrumentation
Prior experience with mammalian cell culture

Responsibilities

Set up, maintain, and operate Orbitrap mass spectrometry and associated liquid chromatography systems
Maintain mammalian cell cultures; prepare growth media and expand cells for experiment setup
Execute proteomics sample preparation workflows including protein extraction, fractionation, and LC-MS analysis
Use laboratory automation for sample preparation and processing
Contribute to proteomics and chemoproteomics experiments and support data analysis
Present findings in team and cross-functional meetings; maintain meticulous electronic lab notebook records