proteomics-benchmarks

name	proteomics-benchmarks
version	0.1.0
description	Reference benchmark datasets for proteomics DEA optimization. Contains ground-truth metadata, expected fold-changes, and best-known method configurations. Used by the evaluator to score candidate workflows against known references.

Proteomics Benchmarks

Reference datasets with ground truth for evaluating differential expression analysis workflows.

PXD001819

• Description: UPS1 spike-in, 27 runs, 9 conditions, LFQ, Orbitrap Velos
• Ground-truth proteins: ups1_48_proteins.txt
• Expected log2FC:

Contrast	log2FC
A_vs_B	2.0
A_vs_C	4.32
A_vs_D	7.64
B_vs_C	2.32
B_vs_D	5.64
C_vs_D	3.32

• Best-known configuration:
  • Method: deqms
  • FDR method: ihw
  • Imputation: none
  • Metrics: AUC 0.996, TP 47, FP 1