Founding Computational Scientist, Open Proteomics Platform

Deliverome Project; Cambridge (MA); On-site; USD 140,000 - 210,000; Full time

Benefits offered by this job

Health benefits

Retirement plan

Founding team role

Open science culture

Job summary

Deliverome Bio is building a pioneering open atlas of surface protein abundance. We seek a scientist to own the computational proteomics platform, from pipelines and data infrastructure to QC and user-facing tools for bench scientists.

You will help shape data models, provenance, and reprocessing strategies while collaborating with a founding team to publish and share methods and resources. You will work with LC-MS/MS workflows (Evosep LC, Orbitrap Astral Zoom), design scalable analysis, and

Qualifications

• PhD in computational biology, computer science, proteomics, or a related field, or equivalent depth built in industry
• Deep hands-on experience analyzing large-scale bottom-up proteomics data with fluency in at least one modern search and quantification stack
• Experience running analyses at scale, cloud or local, using containerized workflows (Nextflow, WDL, Snakemake)
• Working command of quantitative proteomics statistics: normalization, batch effects, missing value structure in DIA vs DDA, protein inference, FDR estimation
• Proficiency in Python and version control with git/GitHub, including releasing tagged, reproducible pipelines

Responsibilities

• Build, containerize, and maintain pipelines for bottom-up LC-MS/MS analysis, DIA and DDA across hundreds to thousands of files
• Own the stack decisions: search and quantification software, workflow orchestration, compute and storage architecture, and cost
• Build the data model and provenance layer, covering sample and run metadata, parameter capture, versioned reprocessing
• Make reprocessing routine, so that improved methods are applied across the full corpus and not only to new data
• Design the quantification strategy for comparability across cell types and experiments
• Implement differential and ranking statistics with error control
• Move toward absolute or ratio-anchored abundance estimates with clear assumptions
• Explore data completeness across cell and tissue types for atlas development
• Build the atlas as a versioned, queryable resource with annotation and topology integration
• Deposit data, co-author methods papers, release pipelines publicly
• Reanalyze published datasets to benchmark and improve results
• Review runs to diagnose where failures likely sit with wet-lab context

Skills

Platform building

Reproducible pipelines

Python

Git / GitHub

Education

PhD in computational biology or related field

Tools

Spectronaut

DIA-NN

FragPipe / MSFragger

AlphaDIA

MaxQuant

Skyline

Job description

Deliverome Bio is building a pioneering open atlas of surface protein abundance. We seek a scientist to own the computational proteomics platform, from pipelines and data infrastructure to QC and user-facing tools for bench scientists.

You will help shape data models, provenance, and reprocessing strategies while collaborating with a founding team to publish and share methods and resources. You will work with LC-MS/MS workflows (Evosep LC, Orbitrap Astral Zoom), design scalable analysis, and