Research Specialist - Mass Spectrometry

About the Role:  

We are seeking a highly skilled and motivated Research Specialist with advanced expertise in mass spectrometry-based data analysis, particularly in quantitative label-free and/or stable isotope labeling proteomics data analysis, global and targeted metabolomics and lipidomics, MS imaging, as well as crosslinking mass spectrometry (XL-MS). The successful candidate will play a central role in the computational and analytical components of research projects, apply state-of-the-art bioinformatics tools, quantitative analysis strategies, and multi-omics data-integration approaches to support a wide range of biological research programs. Although this is a data-focused role, wet-lab proficiency—including sample handling, operation and method setup on Orbitrap Tribrid instrument are highly valued and considered a strong asset. 

About the Mass Spectrometry Department:  

The mass spectrometry department at HHMI, Janelia Research Campus is a new shared resource founded in 2024, which is dedicated to advancing scientific research and innovation in the field of proteomics, metabolomics, lipidomics and many more. We are equipped with pioneering instruments and solutions to facilitate the study of the dynamics, structures, functions, and interactions of various biomolecules which may correlate to cellular dynamics, neural and behavioral mechanisms.  

What we provide:  

• A competitive compensation package, with comprehensive health and welfare benefits.  

• A supportive training environment with opportunities to participate in scientific workshops and conferences.

• Collaborative and innovative work environment with opportunities to make a meaningful impact on scientific research and discovery. 

• Amenities that enhance work-life balance such as on-site childcare, free gyms, available on-campus housing, social and dining spaces, and convenient shuttle bus service to Janelia from the Washington D.C. metro area. 

What you’ll do:  

• Working under the direct supervision of the Department Director, you will serve as a data-analysis specialist with growing independence in designing, executing, interpreting and visualizing complex mass-spectrometry–based experiments.  

• Lead and support in-depth analysis of DIA and DDA proteomic datasets, TMT-based multiplexed proteomics sets, global and targeted metabolomics, lipidomics, XL-MS as well as MS MALDI imaging datasets, using state-of-the-art bioinformatics and statistical tools. 

• Collaborate closely with researchers to guide study design, interpret results, troubleshoot challenging datasets, and contribute to the development and optimization of new mass spectrometry methodologies and workflows. 

• Develop, optimize, and validate computational workflows and data-analysis pipelines, including QC assessment, normalization strategies, spectral library generation, PTM analysis, peptide/protein quantification, metabolite identification, lipid species annotation, and crosslink identification. 

• Integrate multi-omics datasets when appropriate and contribute to biological interpretation in collaboration with project teams. 

• Keep accurate, detailed electronic records of experimental methods, raw and processed data, computational workflows, and analysis outcomes. 

• Help support day-to-day operations of the mass-spectrometry facility, including maintaining laboratory workstations, reporting instrument issues, and ensuring workflows meet high research-quality standards. 

• Train junior personnel or visiting researchers in data-analysis tools, interpretation strategies, and laboratory best practices. 

• Support the department’s commitment to a collaborative, equitable, and inclusive work environment. 

What you bring:  

• Master’s or Ph.D. degree in computing science, computational biology, biochemistry, biology, chemistry, or a closely related field. 

• At least 4 years (BS) or 2 years (MS) of experience in analysis and visualization of proteomics, metabolomics, lipidomics, MS imaging or XL-MS data. 

• Demonstrated expertise in deep data analysis of: DIA proteomics (e.g., DIA-NN, Spectronaut, Skyline), TMT-multiplexed proteomics (e.g., MaxQuant, Proteome Discoverer), Metabolomics and lipidomics datasets (e.g., Compound Discoverer, LipidSearch, MS-Dial), MS imaging (e.g., SCiLS™), Crosslinking MS data (e.g., XlinkX, MeroX) 

• Strong computational aptitude and familiarity with statistics, data visualization, and large-scale data management; experience using R or Python is a plus. 

• Proficiency with mass-spectrometer operating and tuning software; experience with Thermo Xcalibur and Orbitrap Tribrid platforms is highly preferred. 

• Enthusiastic, self-motivated, and able to work both independently and within a collaborative research environment. 

• Excellent organization, communication, and time-management skills. 

• Strong attention to detail, especially in documentation, QC tracking, and method validation and reproducibility. 

• Ability to work effectively as part of a diverse, multidisciplinary team. 

Physical Requirements

Remaining in a normal seated or standing position for extended periods of time; reaching and grasping by extending hand(s) or arm(s); dexterity to manipulate objects with fingers, for example using a keyboard; communication skills using the spoken word; ability to see and hear within normal parameters; ability to move about workspace. The position requires mobility, including the ability to move materials weighing up to several pounds (such as a laptop computer or tablet). Work may involve possible exposure to malodorous vapors, low dose radiation, contamination by toxic chemicals and acids and presence of carcinogenic substances or other hazardous materials.

Persons with disabilities may be able to perform the essential duties of this position with reasonable accommodation. Requests for reasonable accommodation will be evaluated on an individual basis.

Please Note:

This job description sets forth the job’s principal duties, responsibilities, and requirements; it should not be construed as an exhaustive statement, however.  Unless they begin with the word “may,” the Essential Duties and Responsibilities described above are “essential functions” of the job, as defined by the Americans with Disabilities Act.

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