C-COMPASS 2.0 sample session

Sample sessions for the C-COMPASS tool version 2.x (https://doi.org/10.1038/s41592-025-02880-3).

Four different checkpoints from loading the data to the final stistical analysis, based on the dataset from https://zenodo.org/records/13901167:

• sample_session_1_data_loaded.ccompass: The fractionation and total proteome data was loaded, sample information has been assigned, and the marker list was loaded.
• sample_session_2_pretraining.ccompass: The previous session after processing fractionation and total proteome data and matching markers.
• sample_session_3_posttraining.ccompass: The previous session after training the model.
• sample_session_4_final.ccompass: The previous session after predicting proteome and calculating global and class-centric changes.

To load any of these files into C-COMPASS:

1. Download the file
2. Launch C-COMPASS
3. File→Open
4. Choose C-COMPASS zip file type
5. Select the downloaded fiel
6. Open
7. Explore the GUI