Open-source proteomics analysis pipeline

Proteomics analysis.From data todocumented results.

Start with wide-format quantitative tables from DIA-NN or Spectronaut. Use CoPYlot’s open-source tools to run statistical tests, edit figures and export result tables.

Download CoPYlot Product overview

GPL-3.0 license

Proteomics CoPYlot volcano plot of the bundled HEK293 WT versus GRK protein dataset — Bundled HEK293 example · GRK versus WT · 7,490 protein groups

From imported data to reusable results.

Check protein coverage across replicates.

Compare the number of protein groups quantified in each sample. The dashed line marks the 7,490 groups observed across the dataset.

Protein coverage for five WT and five GRK samples, with a reference line for total coverage.

Edit an intensity boxplot.

Compare the distribution of protein intensities by condition. Watch the same plot change as condition colors, median labels and outliers are switched on.

Animated intensity boxplot showing color, median label and outlier settings.

Find proteins that differ between GRK and WT.

Each point is a protein group. The volcano plot pairs the change in abundance with a significance measure adjusted for multiple testing. Labels identify individual genes.

Animated volcano plot of GRK versus WT, highlighting higher and lower protein abundance.

Share the findings. Save the analysis.

The report records the figures, tests and results. A separate CoPYlot savefile lets you reopen the session with its data and settings.

Proteomics CoPYlot · Report excerpt

HEK293 whole-proteome analysis

Wild type versus GRK · Five replicates per condition

1.6 PCA Plot

Data source: Unfiltered, non-imputed protein intensities
Features used: 7,213 of 7,490 protein groups (96.3%) were complete across all samples and showed variation.
Projection: 2D PCA on centered features, colored by condition.

PCA figure from the rendered HEK293 report, showing the five WT and five GRK replicates on the first two principal components.

Share your data in an interactive viewer.

Share the viewer with collaborators or publish it alongside your paper so anyone can look up their protein of interest or develop their own hypotheses in the context of your dataset.

Example data: J. Marx, HEK293 wild-type versus GRK. CC BY 4.0

Choose where the analysis goes

Work locally. Connect AI and sharing only when needed.

Default

On your computer

The desktop app runs a local server and opens in your browser. Your tables stay on your machine.

Optional

An AI assistant

Use a local Ollama or OpenAI-compatible model, or a cloud provider with your own key. Cloud requests include dataset summaries, so local models suit unpublished data.

Optional

A shared viewer

Publish a read-only viewer, or a password-protected portal, so collaborators can explore results without changing them.

The lasting scientific record

Reproducible by design.

CoPYlot records the settings, data snapshot, dependencies and code needed to inspect or rerun an exported result.

No coding experience requiredAuditablePortable

Volcano_Plot.zipDownload demo ZIP

01Volcano_Plot.ipynbopen and rerun the complete analysis02functions.pydependency-closed analysis and plotting code03resources/input.parquetexact captured analysis matrix04resources/metadata.parquetsample and condition mapping05resources/settings.jsonevery plot and analysis selection06resources/original.pngreference output for verification07manifest.jsonhashes, provenance and tool versions08requirements.txtpinned runtime dependencies

# final notebook verificationEvery output is compared with the original.Changed inputs fail their recorded SHA-256 check.

No code required · Executable record · Byte-level verification

Build openly. Work reproducibly.

Release