Proteomic Screening Services

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Introducing Proteome Screening Services

Recent advances in mass spectrometry (MS) and proteomics workflows have dramatically increased the speed, depth, and scalability of proteome analysis. These innovations enable broad proteomic coverage in high-throughput formats suitable for drug discovery and systems biology.

MS-based proteomic screening is a powerful, unbiased approach for identifying degrader targets and assessing selectivity. Unlike traditional assays, it does not require prior knowledge of protein targets—making it ideal for discovering novel degradation events and off-target effects in a single experiment.

Our deep proteome screening platform integrates state-of-the-art automation, high-resolution chromatography, Orbitrap Astral mass spectrometry, and advanced data analysis pipelines. The streamlined workflow enables rapid and reproducible quantification of thousands of proteins across large sample sets.

Workflow Overview

Project Kickoff

Each project starts with a consultation to define sample submission guidelines, timelines, and expectations around data quality and delivery. To streamline downstream processing and analysis, we ask that sample groupings and comparisons be provided at the time of submission.

Cell Type Considerations

We’ve worked with a wide range of cell types—but if yours is new to our workflow, we’ll start with a control plate to assess protein recovery at your target cell count (~40,000 cells per well).

Screening Setup

Once baseline recovery is confirmed and expectations are aligned, we proceed with screening. Our standard format includes 3 compound-treated wells and 3 vehicle control wells per plate, though we’re flexible and happy to accommodate custom layouts.

Data Delivery

Proteomic screening generates dense datasets—each 96-well plate can produce ~400 GB of data. We deliver raw files via your preferred method, with AWS S3 transfers being the most commonly used solution.

Workflow Timing

Sample prep

~24 hours

Data acquisition

~24 hours

Data processing

~24 hours

All samples are processed in the order received. While project timelines may vary based on the submission size, a 2-week turnaround is typical.

Data Analysis and Visualization

After primary processing—protein identification and quantification—secondary analysis is carried out using Python-based workflows in Jupyter notebooks (Pandas, NumPy, SciPy, etc.).

We offer a variety of processed outputs tailored to your goals. Volcano and funnel plots are among the most commonly requested visualizations, but we’re happy to accommodate specific formats or reproduce figures from the literature. Just send over an example, we’ll take it from there.

Downloadable Poster

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Welcome to the New Era of Proteomics

Mass spectrometry-based proteomics has changed dramatically in recent years. Let’s talk about how deep, unbiased proteome screening can accelerate your drug discovery. Please reach out to info@msbioworks.com or call  1-888-960-0650

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