Consultant: Senior Protein​/Peptide Mass Spectrometry Scientist

Consultant:
Senior Protein/Peptide Mass Spectrometry Scientist

Arinale Biosciences Incorporated

Arinale Biosciences is a biotechnology startup operating in stealth mode after recently being spun out of one of New York City’s premier academic medical centers. Occupying a unique position at the nexus of scientific discovery and healthcare, Arinale’s platform for rapid development of paradigm-changing therapeutics will extend the benefits of precision medicine far beyond current limitations and fundamentally improve human. We are helping create a future where every diagnosis is clearer, every decision is more confident, and every patient has more hope.

Guided byvision and powered byinnovation, wewillcatalyzethe discovery and development of a new generation of transformative precision therapies.

We are seeking a senior protein/peptide mass spectrometry scientist to lead experimental design, instrument operation, and data analysis focused on chemoproteomics. Extensive experience in chemical proteomics — activity-based protein profiling, covalent probe chemistry, and chemoproteomic enrichment workflows — is central to this role and considered a critical, must-have qualification, not a supplementary one. A successful candidate will integrate with wet-lab and computational teams, collaborating on sample preparation strategy, method development, and end-to-end interpretation of complex proteomic and chemoproteomic datasets.

Ideal candidates will have hands‑on mastery of the mass spectrometer itself, from tuning and troubleshooting through to spectral interpretation, and will enjoy the creative challenge of translating fragmentation and covalent‑labeling data into confident, well‑quantified protein and peptide identifications.

We are seeking a consultant for an initial 6-month engagement. The position entails several specific deliverables, including development and optimization of protocols for specific chemoproteomic approaches, as well as data acquisition and analyses of a few, select proteomics studies. Potential for continuation as a full-time employee at Arinale Biosciences upon successful completion of consulting contract.

This position is in New York (NY) and requires full-time, in-person work in a laboratory setting.

• Lead chemical proteomics workflows, including activity-based protein profiling (ABPP) and covalent probe/warhead-based target and off‑target identification
• Design and execute chemoproteomic labeling, bioorthogonal click chemistry conjugation, and affinity enrichment workflows to map reactive and ligandable sites across the proteome
• Setup, operate and tune LC-MS/MS platforms (e.g., Orbitrap, Q-TOF, triple quadrupole, ion trap) to ensure optimal sensitivity, resolution, and mass accuracy
• Design bottom-up, top-down, and targeted (MRM/SRM/PRM) proteomics experiments tailored to the biological question
• Select and optimize protease digestion, reduction/alkylation, and chemical or isobaric labeling strategies (e.g., TMT, iTRAQ, SILAC)
• Develop and optimize PTM enrichment workflows (e.g., IMAC/TiO2 phosphopeptide enrichment, immunoprecipitation, glycopeptide enrichment)
• Select and optimize fragmentation methods (CID, HCD, ETD, EThcD) for peptide sequencing and PTM localization Perform database searching, statistical validation (target-decoy FDR, PEP), and quantitative analysis of MS data
• Troubleshoot instrument performance issues, chromatographic coupling problems, and unexpected spectral artifacts
• Generate reports and visualizations summarizing identification, quantification, and PTM localization results
• Collaborate with biologists and computational scientists on experimental design and data interpretation
• Communicate results (oral, written) to colleagues, collaborators, and stakeholders
• Mentor junior scientists and maintain SOPs for sample preparation and instrument operation
• Maintain knowledge of state-of-the-art instrumentation, workflows, and best practices

• PhD in Analytical Chemistry, Biochemistry, Chemical Biology, Proteomics, or a related field, or
• Master’s degree in one of the above fields and 5+…