# id_bruker — MHCquant2 timsTOF identification benchmark subset

Immunopeptidomics **identification** benchmark data (Bruker timsTOF Pro, TOFIMS/PASEF),
selected from the MHCquant2 publication's benign tissue dataset.

## Source
- **Publication:** Scheid et al., *MHCquant2 refines immunopeptidomics tumor antigen discovery*, Genome Biology (2025). doi:10.1186/s13059-025-03763-8
- **PRIDE / ProteomeXchange:** PXD058436 ("benignMHCquant2", timsTOF Pro)

## Selection
For **each HLA class (I and II)**: 5 **low**, 5 **middle**, 5 **high** peptide-yield samples (30 samples), 
**all technical replicates**, both `*.d.tar.gz` (Bruker raw) and `*.mzML`.
Yield = unique identified peptide sequences per sample (class I: `_prediction_result.tsv`; class II: `.tsv`).


## classI samples (unique peptides)
| tier | sample | unique peptides |
|---|---|---|
| low | DN13_Cerebellum_classI | 645 |
| low | DN13_Muscle_classI | 1,253 |
| low | DN13_Aorta_classI | 1,258 |
| low | DN15_Brain_classI | 1,574 |
| low | DN15_Heart_classI | 1,666 |
| middle | DN08_Brain_classI | 8,008 |
| middle | DN08_Thyroid_classI | 8,191 |
| middle | DN15_Thyroid_classI | 8,317 |
| middle | DN15_Pylorus_classI | 8,375 |
| middle | DN09_Pancreas_classI | 8,492 |
| high | DN02_SmallIntestine_classI | 18,472 |
| high | DN12_Liver_classI | 18,472 |
| high | DN13_Corpus_classI | 19,041 |
| high | DN12_Pancreas_classI | 17,571 |
| high | DN02_Spleen_classI | 20,977 |

## classII samples (unique peptides)
| tier | sample | unique peptides |
|---|---|---|
| low | DN08_AdrenalGland_classII | 2,627 |
| low | DN05_Skin_classII | 2,548 |
| low | DN08_Heart_classII | 2,067 |
| low | DN13_Cerebellum_classII | 2,176 |
| low | DN06_Cerebellum_classII | 2,289 |
| middle | DN12_Bladder_classII | 8,996 |
| middle | DN09_Pancreas_classII | 8,475 |
| middle | DN14_Aorta_classII | 8,796 |
| middle | DN12_Liver_classII | 8,901 |
| middle | DN09_Liver_classII | 8,903 |
| high | DN13_Lung_classII | 16,627 |
| high | DN15_SmallIntestine_classII | 16,855 |
| high | DN08_Spleen_classII | 16,909 |
| high | DN13_Corpus_classII | 17,191 |
| high | DN02_Pancreas_classII | 17,911 |