fun_proteomics · Start here

DDA-PASEF · DIA-PASEF · RAW BAF · SERVICE BENCHMARKS

From inputs to protein and gene results

Analyze raw Bruker acquisitions or a quantification matrix. Get every condition comparison, quality control and matched service detection benchmarks. Every matrix is available as CSV and TSV.

1. Install once

Linux and Python 3.11 or newer:

pip install --upgrade fun_proteomics
fun_proteomics install --conda
fun_proteomics doctor

Python environments, requirements and existing runtimes

REAL PUBLISHED LFQ DATA

Try a small complete analysis

Download 12 ubiquitin-affinity samples: four conditions and three experimental replicates per condition. The archive includes quantities, sample assignments, checksums, original source files and attribution.

wget https://github.com/cfarkas/fun_proteomics/releases/download/v0.9.0/ubiquitin-lfq-example.tar.gz
wget https://github.com/cfarkas/fun_proteomics/releases/download/v0.9.0/ubiquitin-lfq-example.tar.gz.sha256
sha256sum -c ubiquitin-lfq-example.tar.gz.sha256
tar -xzf ubiquitin-lfq-example.tar.gz
fun_proteomics setup --project "$PWD/ubiquitin-study" \
  --mode matrix --matrix "$PWD/ubiquitin-lfq-example/proteins.csv" \
  --samples "$PWD/ubiquitin-lfq-example/samples.csv"

Discover the samples, review the four condition columns, confirm the replicate design, then save and run. This uses real quantified data and does not repeat a raw spectrum search.

Step-by-step guide and expected outputs

2. Set up your analysis

Choose one launch method. --project is your output folder. setup --outdir is equivalent. Use a new project for a new analysis.

A) Interactive settings

fun_proteomics setup --project /data/my-study

Choose a matrix, raw-data folder or previous run, and review the output folder.
Click Discover samples, then drag sample cards into condition columns. Add or rename conditions; move exclusions to Unassigned. A sample table can prefill assignments.
Choose independent samples or paired matrix/BAF comparisons with donor IDs. Four conditions produce six condition pairs at each feature level.
Click Save configuration and check, then Run / continue analysis.
Open Results or Matrices · CSV & TSV in the same page.

Keep the terminal open during setup. Browse paths refer to the computer running the analysis.

Inputs, donors, technical injections and SSH browser access

B) Terminal questions

fun_proteomics setup --terminal --project /data/my-study --run

Answer the questions about inputs, conditions, replicate design and output folder. This works over SSH. Omit --run to save and review first.

C) Full command-line options

fun_proteomics setup --non-interactive --project /data/my-study \
  --mode matrix --matrix /data/proteins.csv --samples /data/samples.csv \
  --independent-samples --normalization none \
  --cpus 8 --memory-gib 32 --run

For paired matrix/BAF data, replace --independent-samples with --subject-column donor. Add --service-matrix /data/provider.tsv for a matched service benchmark.

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

Complete options and raw DIA/DDA/BAF commands

3. Find results and continue

my-study/START_HERE.html
my-study/MATRICES.html

The matrix catalogue links directly to CSV and TSV files. Detailed outputs live in results/final_results/.

fun_proteomics --continue /data/my-study

Verified native results and complete BAF searches are reused. Raw PASEF runs resume their Nextflow session.

Output guide · Integrity and recovery

Watch the interactive walkthroughs

Captioned recordings of the actual application. All inputs are synthetic. Use full screen for the clearest view.

REAL MATRIX ANALYSIS

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.

Download MP4 Captions Follow along

TERMINAL / SSH

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.

Download MP4 Actual session transcript Captions

RAW DIA SETUP ONLY

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.

Download MP4 Captions Raw-data setup guide

RAW BAF SETUP ONLY

Raw BAF: technical injections and paired donors

Group technical injections under biological sample IDs, assign donors, choose an output folder, and review all six condition pairs. Synthetic placeholders are never searched.

Download MP4 Captions BAF analysis guide

Raw BAF and service benchmarks

fun_proteomics install --baf
fun_proteomics setup --mode baf --project /data/my-baf-study

Group technical injections under one biological sample ID and enter donor IDs for paired comparisons.

Raw BAF guide · Benchmark any run against a service

Full execution and service comparisons

The EV_PPC raw BAF analysis completed all 48 acquisitions, retained all four donors, and tested every condition pair at protein and gene levels. Review the execution evidence and matched-sample detection benchmarks across DDA, DDA+, DIA and BAF runs.

Read the full execution report and benchmark table