Scientist II or Senior Scientist, Protein Analytics

Job Description

Job Description

Role Location: Waltham, MA

The Company
We are Alloy Therapeutics — a biotechnology ecosystem and Product Development Organization (PDO) empowering the global scientific community to make better medicines together. Through a community of partners, we democratize access to pre-competitive tools, technologies, services, and company creation capabilities that are foundational for discovering and developing therapeutic biologics. The company facilitates affordable, non-exclusive access to the entire drug discovery community from academic scientists, small and medium biotech, to the largest biopharma. At Alloy, we believe our industry should compete on getting the best drugs to patients as quickly as possible, not exclusive access to the best platforms. As a reflection of our relentless commitment to the scientific community, we reinvest 100% of our revenue in innovation and access to innovation. May the Best Drug Win. 

Alloy has evolved from a startup into a global product development organization operating 11 divisions across 5 research sites in 4 countries on 3 continents. Our model - Integrated Independence - combines centralized capabilities with entrepreneurial operating divisions. Successful members thrive in our shared culture of accountability, deliberate trust, and open communication. As a team we aspire to work together to exceed expectations and collectively contribute across the global organization to always maintain our nimble, startup culture. 

At Alloy, we have an ethos of "Mentorship-By-Apprenticeship" in all of our positions. We strive to have workers in the office when needed to interact organically and face-to-face. Of course, as a lab-based operation, our cells and animals grow 7 days a week, 365 days per year. We respect and value our colleagues for their hard work that requires them to be in the lab every day. We ask our people who have more flexible accommodations to appreciate their colleagues who have less flexibility. We are all one team!

About the Role
Alloy’s Protein Analytics group, within the Alloy Antibody Powered Division, provides analytical support across all analytical activities, including assay development, quality control, high-throughput screening, and detailed characterization of monoclonal and multispecific antibodies, TCRs, TCR mimics, and other modalities.

We are seeking a highly motivated Scientist or Senior Scientist to conduct biophysical screening and analytical characterization as part of our dynamic, fast-paced biotech team. In this role, you will design & execute high-throughput screening, stability, forced degradation, and pre-formulation experiments using various analytical techniques. You will work collaboratively in a matrixed environment to advance biologics discovery and support rapid, data-driven decision-making.

This role will report to the Head of Protein Analytics and offers significant autonomy, with ownership of multiple stakeholders, projects, and tasks in a dynamic start-up environment, while maintaining the pace and standards of Alloy.

How You'll Drive Impact

• Execute : Independently design and execute high-throughput screening, stability, forced degradation, and pre-formulation studies to characterize monoclonal and multispecific antibodies and other modalities at various stages of development.
• Develop : Develop, validate, and optimize advanced analytical methods and workflows for high-throughput screening, stability, forced degradation, and impurity characterization, establishing best practices across the team. 
• Deliver : Drive later-stage characterization efforts end-to-end, from experimental design through data interpretation, delivering robust stability and developability packages that inform key program decisions.
• Collaborate : Partner across multi-disciplinary teams and Alloy sites, and supervise and mentor junior scientists, reviewing their experimental design and data to ensure quality and consistency.
• Communicate : Clearly present complex data, conclusions, and recommendations to internal stakeholders and cross-functional teams.

Key Responsibilities 

• Independently design and execute high-throughput screening, stability, forced degradation, and pre-formulation studies using LC-MS, CE-SDS, CZE/cIEF, DLS, SPRi, BLI, and chromatographic techniques (SEC, HIC, etc.).
• Lead later-stage characterization efforts, including high-concentration stability and impurity characterization studies, to support developability and formulation decisions.
• Develop and validate new analytical methods, and optimize existing workflows for improved throughput, sensitivity, and reproducibility.
• Supervise and mentor junior scientists: providing technical guidance, reviewing experimental designs and data, and supporting their professional development.
• Maintain analytical instrumentation and ensure best practices and troubleshooting protocols are followed across the team.
• Support protein binding assays using BLI (Octet) and SPRi (Carterra LSA), as needed.
• Present experimental data, interpretations, and recommendations during team and cross-functional meetings.
• Ensure timely and successful execution of project activities, proactively identifying and resolving technical challenges.
• Maintain detailed and accurate laboratory records and ensure laboratory organization and compliance with safety protocols.

Qualifications

• Ph.D. with at least 2 years of relevant industry experience, or M.S. with at least 6 years of relevant industry experience.  
• Proven track record of expertise in various protein analytical and/or biophysical assessments.
• Hands-on experience with LC-MS, CE-SDS, CZE or cIEF, DLS, and various chromatographic techniques such as SEC, HIC, etc.  
• Experience with high concentration stability, forced degradation, and / or impurity characterization studies, preferably within an industry setting.
• Experience in the maintenance and troubleshooting of analytical instrumentation. 
• Preferred experience with protein-binding (BLI, SPRi), and/or cell-binding (Flow Cytometry). 
• Demonstrated ability to troubleshoot and maintain analytical instrumentation.
• Excellent written and verbal communication skills, with the ability to clearly present complex scientific data.
• Ability to effectively multitask and deliver results within project-driven timelines.
• Strong sense of ownership, urgency, persistence, and scientific integrity.
• Excellent organization, clear communication and teamwork abilities in a multidisciplinary setting. 
• Thrives working on a team and collaborating with others to achieve project goals.
• Enjoys a dynamic and exciting work environment. 
• Detail oriented, with rigorous scientific thinking and a passion for drug discovery to improve patients’ lives.

Taking Care of Our People
We support the individuality of what people need to do outside of work to empower them to do their best at work. While you focus on making better medicine together , we focus on programs and benefits that support a diverse and growing team. Whether you’re single, in a growing family, or nearing retirement, Alloy offers a variety of comprehensive and competitive benefits starting from day one.

Compensation

• Competitive base and equity compensation commensurate with level of experience and independence
• 401(k) company match

Health & Family

• Generous personal and family medical, dental and vision benefits with 100% of premiums and deductibles covered
• Company-paid disability (STD, LTD) and life insurance
• Paid parental leave
• Family planning support up to $45,000 (e.g., IVF/PGT, adoption, surrogacy, egg retrieval)

Unique Perks

• Unlimited PTO (paid time off) and flexible schedules
• Annual stipend for continuing education with commitment to your career through individualized professional development plan
• Wellness and Extensive Employee Assistance Program (EAP) including resources for mental wellness

Pay Transparency
At Alloy Therapeutics, we believe in fostering trust and open communication. For this role, the estimated range is $130,000 - $160,000, with the final offer based on factors like your experience, skills, and alignment with our needs.

Additionally, this role is eligible for equity compensation, reflecting our commitment to shared success as we work together to make better medicines.

We are proud to offer competitive compensation and benefits, aiming to support our team’s professional and personal well-being. If you have any questions about pay or benefits, we’re here to help.

Alloy Therapeutics is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, national origin, sex, sexual orientation, gender identity, veteran status, disability, or other legally protected status.  If you are unable to submit an application because of incompatible assistive technology or a disability, please contact us at View email address on ziprecruiter.com .  We will make every effort to respond to your request for disability assistance as soon as possible.

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