Associate Principal Scientist, Mass Spectrometry

Job Description

The Analytical Enabling Capabilities organization in West Point, PA is seeking a motivated scientist with technical expertise in mass spectrometry-based protein, protein conjugation or oligonucleotides or polysaccharide characterization. In addition to mass spectrometry skills, we are also seeking candidates with strong scientific leadership, proteomics and data science skills.

The ideal candidate will have a track record of advancing the pharmaceutical development of vaccines with mass spectrometry, as well as driving scientific excellence through external presentations and publications. Additionally, the candidate will have advanced knowledge in both analytical experimental design and vaccines pipeline programs. Finally, this Associate Principal Scientist will be a partner in problem solving, building leadership, and driving collaboration both internally and externally.

Primary Responsibilities

• Develop and Perform LC-MS based assays including peptide mapping, intact mass, native mass spectrometry, proteomics, higher order structure, and host cell protein analysis or oligonucleotides or polysaccharide characterization for vaccines programs.

• Advance mass spectrometry methodology for peptide mapping, intact mass, native mass, HDX, sequence variants, glycan analysis, quantitative analysis, and host cell protein analysis.

• Represent the mass spectrometry group in project teams.

• Author technical reports and scientific presentations.

• Explore and develop new technologies to advance the field of mass spectrometry.

• Perform data processing with Genedata or other biopharma data interpretation software.

• Demonstrate effective multitasking, prioritization and problem-solving skills in the planning and execution of experiments.

• Scientific leadership and mentorship of scientists.

• Champion compliance and safety as a leader both within and outside the laboratory.

Education Minimum Requirement:

• PhD in Analytical Chemistry or Chemistry or relevant degree in mass spectrometry plus 5+ years of relevant experience in pharmaceutical industry

• Candidates with MS in degree plus 8+ years or BS degree plus 12+ years of relevant industry experience

Required Experience and Skills

• A breadth and depth of analytical and vaccines development understanding, including protein, protein conjugates, oligonucleotides and polysaccharides.

• Experience in conducting mass spectrometry experiments, including sample preparation and optimization, liquid chromatography separation, mass spectrometer operation and maintenance, data interpretation, and analysis.

• Extensive knowledge of Thermo, Sciex, Agilent and Waters instruments.

• Familiarity with Genedata or other biopharma MS software.

• Excellent verbal and written communications skills, as demonstrated through high impact scientific publications and presentations. 

• Experience mentoring junior scientists in pharmaceutical development

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Preferred Experience and Skills

• Expertise in multiple reaction monitoring based quantitative analysis for vaccines development.

• Expertise in complex glycan analysis.

• Familiarity with R programming language for data processing, statistics and visualization.

• Advanced knowledge of electronic laboratory notebook applications and good documentation practices.

Required Skills:

Analytical Chemistry, Analytical Method Development, Assay Development, Biological Assay Development, Cell-Based Assays, Chromatographic Techniques, High Resolution Mass Spectrometry (HRMS), Laboratory Documentation, Liquid Chromatography-Mass Spectrometry (LC-MS), Mass Spectrometry (MS), Mass Spectrometry Analysis, Peptide Mapping, Process Analytical Technology (PAT), Protein Analysis, Proteomics, R Programming, Secondary Ion Mass Spectrometry (SIMS), Spectrometry, Vaccine Development

Preferred Skills:

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As an Equal Employment Opportunity Employer, we provide equal opportunities to all employees and applicants for employment and prohibit discrimination on the basis of race, color, age, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability status, or other applicable legally protected characteristics.  As a federal contractor, we comply with all affirmative action requirements for protected veterans and individuals with disabilities.  For more information about personal rights under the U.S. Equal Opportunity Employment laws, visit:

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The salary range for this role is

$142,400.00 - $224,100.00

This is the lowest to highest salary we in good faith believe we would pay for this role at the time of this posting. An employee’s position within the salary range will be based on several factors including, but not limited to relevant education, qualifications, certifications, experience, skills, geographic location, government requirements, and business or organizational needs.

The successful candidate will be eligible for annual bonus and long-term incentive, if applicable.

We offer a comprehensive package of benefits.  Available benefits include medical, dental, vision healthcare and other insurance benefits (for employee and family), retirement benefits, including 401(k), paid holidays, vacation, and compassionate and sick days. More information about benefits is available at https://jobs.merck.com/us/en/compensation-and-benefits.

You can apply for this role through https://jobs.merck.com/us/en (or via the Workday Jobs Hub if you are a current employee). The application deadline for this position is stated on this posting.

San Francisco Residents Only: We will consider qualified applicants with arrest and conviction records for employment in compliance with the San Francisco Fair Chance Ordinance

Los Angeles Residents Only: We will consider for employment all qualified applicants, including those with criminal histories, in a manner consistent with the requirements of applicable state and local laws, including the City of Los Angeles’ Fair Chance Initiative for Hiring Ordinance

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Merck & Co., Inc., Rahway, NJ, USA, also known as Merck Sharp & Dohme LLC, Rahway, NJ, USA, does not accept unsolicited assistance from search firms for employment opportunities. All CVs / resumes submitted by search firms to any employee at our company without a valid written search agreement in place for this position will be deemed the sole property of our company.  No fee will be paid in the event a candidate is hired by our company as a result of an agency referral where no pre-existing agreement is in place. Where agency agreements are in place, introductions are position specific. Please, no phone calls or emails. 

Employee Status:

Regular

Relocation:

VISA Sponsorship:

Travel Requirements:

Flexible Work Arrangements:

Not Applicable

Shift:

Valid Driving License:

Hazardous Material(s):

Job Posting End Date:

08/22/2026

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