Founding Computational Scientist, Proteomics

Deliverome Project; Cambridge (MA); Presencial; USD 140 000 - 210 000; Tempo integral

Vantagens oferecidas por esta oferta de emprego

Health benefits

Retirement plan

Founding team role

Open science culture

Resumo da oferta

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

Qualificações

• 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

Responsabilidades

• 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

Conhecimentos

Platform building

Reproducible pipelines

Python

Git / GitHub

Formação académica

PhD in computational biology or related field

Ferramentas

Spectronaut

DIA-NN

FragPipe / MSFragger

AlphaDIA

MaxQuant

Skyline

Descrição da oferta de emprego

About The Deliverome Project

Deliverome Bio is a nonprofit startup building a first-of-its-kind open atlas of surface protein abundance and internalization. We’re hiring a founding team to generate the data that could expand what targeted therapies can reach.

About The Deliverome Project

Deliverome Bio is a nonprofit startup building a first-of-its-kind open atlas of surface protein abundance and internalization. We’re hiring a founding team to generate the data that could expand what targeted therapies can reach.

The Role

You will build and own the computational side of our proteomics platform: the pipelines, analysis, and data infrastructure that turn raw spectra from surface-enrichment experiments into quantitative measurements of the human surfaceome that we can compare across experiments and release publicly. This role is primarily scientist-facing. The people at the bench are who you serve first, and much of the work is building QC, reports, and result formats they can use directly without waiting on you. You will also contribute to our broader computational and data infrastructure, including how samples, metadata, and files are tracked, because the person who understands the data model should help decide how the data gets recorded in the first place.

We have an Evosep LC and an Orbitrap Astral Zoom, and we plan to run them at high sample throughput across many cell types and conditions. The data volumes and reprocessing demands that come with that need to be planned for from the beginning rather than handled once we are behind. We are flexible on whether compute lives in the cloud, on local hardware, or both. What we care about is scale, reproducibility a year later, and being able to release everything we generate. We currently run Spectronaut and are open to changing or adding to it, and we would value your perspective on the tradeoffs between commercial and open-source stacks at this throughput.

We also need someone who can diagnose the full workflow, not only the analysis. Surface proteomics can fail at labeling chemistry, enrichment specificity, digestion, chromatography, acquisition, search parameters, normalization, and statistics. We are looking for someone who can review a set of runs, say where the problem most likely sits, and propose the experiment that distinguishes between the remaining possibilities. That means knowing the wet lab well enough to push on experimental design while it is being decided, not after the samples are made.

This is a rare opportunity to build a public data resource from the first sample onward. No standard exists for how surfaceome abundance and internalization data should be quantified, QC'd, and compared across cell types and labs, and you will have unusual latitude to set one. Everything you build, including pipelines, spectral libraries, QC metrics, benchmarks, and the atlas itself, will be openly released and used by drug developers and academic labs worldwide. Like all of our founding hires, you will have a direct line to the co-founders and a genuine say in how the platform is built. You will gain practical, shareable expertise across large-scale MS analysis, research data infrastructure, and open data release that flexibly advances your career in either industry or academia.

What You Will Do

Analysis infrastructure at scale

• Build, containerize, and maintain pipelines for bottom-up LC-MS/MS analysis, DIA and DDA, that run reproducibly 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, and the ability to answer which pipeline version produced a given number a year later
• Make reprocessing routine, so that improved methods are applied across the full corpus and not only to new data

Quantification, statistics, and the atlas

• Design the quantification strategy for comparability across cell types and experiments, including normalization, batch structure, missing value handling, and protein inference and rollup
• Implement differential and ranking statistics with error control that holds up in review and in reuse by others
• Move toward absolute or ratio-anchored abundance estimates where the biology calls for it, and be explicit about the assumptions behind any copies-per-cell number
• Explore data completeness across cell and tissue types to understand where more data is needed, or when aspects of the atlas are sufficiently statistically empowered
• Build the atlas as a versioned, queryable resource with annotation and topology integration, confidence tiers, and a clear separation between what we measured and what we inferred

Scientist-facing tools and research infrastructure

• Build QC reports, run-level dashboards, and result formats that let bench scientists check and interrogate their own data
• Partner with lab operations on the infrastructure upstream of analysis, including sample and cell line tracking, electronic records, metadata capture at the point of experiment, and file handoff conventions
• Own storage, backup, and data lifecycle for large instrument datasets, including what stays available, what gets archived, and what gets deposited
• Contribute to our general computational tooling as needs come up, and be someone colleagues can bring a data problem to

Integration and open science

• Deposit raw and processed proteomics data to ProteomeXchange/PRIDE or MassIVE with metadata that makes reuse practical, and facilitate deposition of sequencing data to GEO and SRA
• Co-author methods and resource papers, and release pipelines and analysis code publicly
• As we scale and publish our data, integrate proteomic abundance with pooled screening readouts, transcriptomic references, and public surfaceome resources to produce interpretable target rankings and open data viewers
• Reanalyze published surfaceome and cell-surface capture datasets to benchmark our own results and to build on work the field has already done

Required

What We Are Looking For

• 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 (Spectronaut, DIA-NN, FragPipe/MSFragger, AlphaDIA, MaxQuant, Skyline). We run Spectronaut today, but experience matters more to us than the specific tool
• Experience running analyses at scale, cloud or local, using containerized and orchestrated workflows (Nextflow, WDL, Snakemake, or similar)
• Working command of quantitative proteomics statistics: normalization, batch effects, missing value structure in DIA versus DDA, protein inference, and FDR estimation
• Proficiency in Python and version control with git/GitHub, including releasing tagged, reproducible pipelines

Highly valued

• Experience with AWS (preferred) or equivalent, including object storage lifecycle management and batch or spot compute for large reprocessing jobs
• Demonstrated ability to reason about the upstream experiment, including enrichment chemistry, sample preparation, LC, and instrument behavior, well enough to tell whether a failure is biological, chemical, or computational
• Experience supporting bench scientists directly by building tools they can run themselves
• Experience with electronic lab notebooks, LIMS, or sample tracking systems, and views on how to capture metadata in a busy lab
• Building data resources that outside groups use: portals, APIs, versioned releases, FAIR metadata
• Integration with orthogonal data types, including pooled screens, transcriptomics, membrane topology prediction, and existing surfaceome annotation sets
• Experience with or interest in AI coding tools (Claude Code, Codex) as part of daily work

Who You Are

• You're a platform builder: you think about reproducibility, documentation, and what it takes for someone else to run your pipeline
• You care about getting the measurement right, not just getting a number: you know what a given search setting, normalization choice, or FDR method assumes
• You go upstream: when results look wrong you ask about the labeling reaction and the chromatography, not just the code
• You build for the scientists around you, and would rather ship a tool a colleague can run than answer the same request every week
• You know how to define the minimum viable analysis that answers this week's question while building toward a dataset that stays useful for a decade
• You want your work to be adopted and reused by others, and your time to go towards problems that impact society
• You thrive in a small, high-trust team where everyone's contributions are visible and decisions are made fast, and where accelerating science should never be perceived as stepping on toes

Level and Title

We are hiring at the Scientist through Principal Scientist level depending on capability and experience, and we prefer candidates who have built a platform or data product in industry. What matters is depth in large-scale MS data analysis, the judgment to make an analysis reproducible and releasable, and enough experimental fluency to tell us what isn't working and why.

What We Offer

• Competitive salary benchmarked to industry rates
• Full benefits including health, dental, and retirement
• A founding team role: your decisions will shape the platform and the organization
• Open science by design: your work will be published and used globally
• Unprecedented collaboration with world-class advisors across proteomics, functional genomics, targeted delivery, and AI
• A culture that values rigor, transparency, and speed, but doesn’t mistake busyness for productivity