Exporting Results
ProtSpace allows you to export publication-ready figures, raw data, and protein IDs.
Export Button
Click Export in the control bar to see available formats:
| Format | Description |
|---|---|
| PNG | Raster image of the current view with legend |
| PDF document of the current view with legend | |
| Protein IDs | Text file with newline-separated identifiers |
| Parquet | .parquetbundle file with all data and optional settings |
Image Export (PNG / PDF)
When PNG or PDF is selected, you have two export paths:
Figure Editor (Recommended)
Click Figure Editor to open a full-screen editor with live preview. This is the primary workflow for creating publication-quality figures. See the Figure Editor guide for full documentation.
Key features:
- Journal presets for Nature, Science, Cell, PNAS, PLOS, and presentations
- Photoshop-style Dimensions panel — Width/Height/DPI, unit toggle (px/mm/in/cm), Resample on/off, aspect-lock chain
- Overlays — circles, arrows, and text labels to annotate your figure
- Zoom insets — true geometric magnification with a per-inset Dot size slider
- Legend customization — position, font size in pt or px, columns, free-floating placement
- Click-to-select + Delete/Backspace — click an overlay or inset (canvas or sidebar) and press Delete to remove it
- Persistent settings — your layout is saved to localStorage and optionally embedded in
.parquetbundlefiles - Print-correct output — PNG includes pHYs DPI metadata; PDF page size is mm-accurate
Quick Export
Click Quick Export to download an image immediately using default or previously saved settings. No preview — useful when you've already configured the Figure Editor and want the same output again.
Parquet Export
Export a .parquetbundle file that can be loaded back into ProtSpace or shared.
- Include legend settings: Saves your current legend customizations (colors, shapes, ordering, visibility, palette) inside the file. Anyone who loads it will see the same visual configuration.
- Figure editor settings: When legend settings are included, the Figure Editor state (dimensions, DPI, legend layout, overlays, insets) is also saved. This lets you reopen the Figure Editor exactly where you left off.
Protein IDs Export
Exports a plain text file with one protein ID per line. Useful for downstream analysis.
What Gets Exported
| State | Exported Data |
|---|---|
| Proteins isolated | Only isolated proteins |
| No isolation | All proteins |
Use isolation to export specific subsets.
Next Steps
- Figure Editor - Full guide to the publication figure editor
- FAQ - Common questions
- Data Format Reference - Understanding the file format