fun_proteomics

A) Interactive settings

Watch the embedded walkthrough above. Open the browser with fun_proteomics setup, then make your choices in the page.

1. Choose a matrix, raw-data folder or previous run, and review the output folder.
2. Click Discover samples, then drag sample cards into condition columns. Add or rename conditions; move exclusions to Unassigned. A sample table can prefill assignments.
3. Choose independent samples or paired matrix/BAF comparisons with donor IDs. Four conditions produce six condition pairs at each feature level.
4. Click Save configuration and check, then Run / continue analysis.
5. 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

Example input files (illustrative intensity values):

samples.csv — one row per sample:

sample_id,condition
C1,Control
C2,Control
T1,Treatment
T2,Treatment

proteins.csv — one row per protein group:

Protein.Group,Genes,C1,C2,T1,T2
P04637,TP53,120000,135000,260000,245000
P60709,ACTB,480000,505000,490000,510000
P02768,ALB,90000,85000,,100000

Each sample_id must exactly match a quantity column in proteins.csv. Use non-log-transformed intensities; leave missing measurements blank. Genes is optional: include gene symbols here or supply a matching FASTA with GN= annotations for gene-level results.

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

Protein.Group	Genes	C1	C2	T1	T2
P04637	TP53	120000	135000	260000	245000
P60709	ACTB	480000	505000	490000	510000

fun_proteomics check --config /data/my-study/config/run.json
fun_proteomics run --config /data/my-study/config/run.json

{
  "project": "/data/my-study",
  "mode": "matrix",
  "matrix": "/data/proteins.csv",
  "samples": "/data/samples.csv"
}

Complete options and raw DIA/DDA/BAF commands