Browser: from a matrix to all-pairs results
Discover matrix samples, drag them into three conditions, run every pair, open CSV/TSV matrices, and reuse the completed results.
One project, from inputs to results
Analyze raw Bruker acquisitions or an existing quantification matrix. Get protein and gene matrices, every condition comparison, quality control and a detection benchmark against your service provider. Every matrix is available as CSV and TSV.
The execution and documentation follow the setup/check/run pattern used by OncoTracer.
1. Install once
Use Linux and Python 3.11 or newer. Create a Python environment, install the package, then prepare the analysis tools.
python3 -m venv proteomics-env source proteomics-env/bin/activate pip install fun_proteomics fun_proteomics system --path /data/my-study fun_proteomics install --conda fun_proteomics doctor
Already have the tools? Reuse an existing R library or workflow runtime. Registered DDA archives are supplied separately. Installation details
2. Set up your study
fun_proteomics setup --project /data/my-study
- Choose your input: a matrix, raw DIA, raw DDA or a previous run.
- Click Discover samples, then drag cards into condition columns. Add or rename conditions; return cards to Unassigned to exclude them. Keep all-versus-all comparisons and confirm independent biological samples when appropriate.
- Select Save configuration and check, then Run / continue analysis.
Keep the launcher terminal open for setup. After launch, the analysis can continue if the page closes. Reopen the same project to see progress.
Prefer terminal questions or SSH?
fun_proteomics setup --terminal --project /data/my-study --run
The browser and terminal use the same saved settings. Omit --run to review first.
Check and run saved settings
fun_proteomics check --config /data/my-study/config/run.json fun_proteomics run --config /data/my-study/config/run.json
Try the synthetic example · Your own data, sample tables and SSH access
Watch the interactive walkthroughs
Captioned recordings of the actual application. All inputs are synthetic. Use full screen for the clearest view.
Terminal: interactive launch and continuation
Follow the questions and then reuse the completed project with --continue. This replays an actual terminal session at a readable pace.
Raw DIA: scan acquisitions and save an analysis
Scan folders, drag acquisition cards into conditions, select a FASTA and check the project. This demo uses synthetic acquisition metadata and stops before spectrum searching.
3. Find your matrices
Open these shortcuts in your project:
my-study/START_HERE.html my-study/MATRICES.html
The matrix catalogue links to both CSV and TSV. Detailed outputs live under results/final_results/.
Three conditions produce three protein comparisons and three gene comparisons when unambiguous gene mappings are available.
4. Continue whenever needed
fun_proteomics --continue /data/my-study
Completed native results are checked and reused. Damaged reporting is rebuilt from verified inputs into a new generation. Raw workflows reuse their saved Nextflow work/cache.
Changed inputs require a new project. Previous outputs remain available.