De novo peptide sequencing tools benchmark
benchmark · DDA · 1 version · 1 paper
The benchmark’s own ProteomeXchange deposit, which is where its public evaluation data lives as one citable object.
| Kind | benchmark |
| Acquisition | DDA |
The benchmark’s own ProteomeXchange deposit, which is where its public evaluation data lives as one citable object.
Versions
as deposited
Where it lives:
- MassIVE · MSV000096182
The 86 datasets denovo_benchmarks evaluates on
Every dataset the living benchmark scores each tool on, as its repository names them, with the group used for the heatmap on the main page and how many tools have a result there. Most tools ran on all of them; a partial one is left out of the cross-dataset ranking.
| Dataset | Category | Group | Tools |
|---|---|---|---|
| human_herceptin_aspn | Herceptin | Antibody | 18 |
| human_herceptin_chymotrypsin | Herceptin | Antibody | 18 |
| human_herceptin_gluc | Herceptin | Antibody | 18 |
| human_herceptin_lysc | Herceptin | Antibody | 18 |
| human_herceptin_lysn | Herceptin | Antibody | 18 |
| human_herceptin_trypsin | Herceptin | Antibody | 18 |
| human_mAb_aspn | mAb | Antibody | 18 |
| human_mAb_chymotrypsin | mAb | Antibody | 18 |
| human_mAb_trypsin | mAb | Antibody | 18 |
| mouse_mAb_aspn | mAb | Antibody | 18 |
| mouse_mAb_chymotrypsin | mAb | Antibody | 18 |
| mouse_mAb_trypsin | mAb | Antibody | 18 |
| human_multiprotease_aspn | Multiprotease | Digestion | 18 |
| human_multiprotease_chymotrypsin | Multiprotease | Digestion | 18 |
| human_multiprotease_gluc | Multiprotease | Digestion | 17 |
| human_multiprotease_lysc | Multiprotease | Digestion | 18 |
| human_multiprotease_lysn | Multiprotease | Digestion | 18 |
| human_multiprotease_trypsin | Multiprotease | Digestion | 18 |
| human_HLAI | Immunopeptidomics | HLA / MHC | 18 |
| human_HLAII | Immunopeptidomics | HLA / MHC | 18 |
| human_MHCI | Immunopeptidomics | HLA / MHC | 18 |
| mouse_MHCI | Immunopeptidomics | HLA / MHC | 18 |
| mouse_MHCII | Immunopeptidomics | HLA / MHC | 18 |
| human_agilent | Instrument | Instrument | 18 |
| human_astral | Instrument | Instrument | 18 |
| human_jurkat | Instrument | Instrument | 18 |
| staphylococcus_aureus_timstof | Instrument | Instrument | 18 |
| LFQ_orbitrap | LFQ | Instrument | 18 |
| LFQ_sciex | LFQ | Instrument | 18 |
| LFQ_timstof | LFQ | Instrument | 18 |
| multitool_orbitrap | Multitool | Instrument | 18 |
| multitool_sciex | Multitool | Instrument | 18 |
| 9_species_apis_mellifera | 9 species | Organism | 18 |
| 9_species_bacillus_subtilis | 9 species | Organism | 18 |
| 9_species_candidatus_thiodiazotropha | 9 species | Organism | 18 |
| 9_species_human | 9 species | Organism | 18 |
| 9_species_methanosarcina_mazei | 9 species | Organism | 18 |
| 9_species_mus_musculus | 9 species | Organism | 18 |
| 9_species_saccharomyces_cerevisiae | 9 species | Organism | 18 |
| 9_species_solanum_lycopersicum | 9 species | Organism | 18 |
| 9_species_vigna_mungo | 9 species | Organism | 18 |
| animal_invertebrate | Animal | Organism | 18 |
| animal_mammal_1 | Animal | Organism | 18 |
| animal_mammal_2 | Animal | Organism | 18 |
| CAMPI_F07 | CAMPI | Organism | 18 |
| CAMPI_S11 | CAMPI | Organism | 18 |
| fungus | Non-model organism | Organism | 18 |
| plant | Non-model organism | Organism | 18 |
| hela_single_cell | Single cell | Other | 18 |
| hela_single_cell_2 | Single cell | Other | 18 |
| hela_single_cell_2_bulk | Single cell | Other | 16 |
| hela_single_cell_bulk | Single cell | Other | 15 |
| UPS | UPS | Other | 18 |
| iPRG | iPRG | Other | 18 |
| iPRG_2015 | iPRG | Other | 18 |
| 21PTMs_Kmod | 21 PTMs | PTMs | 18 |
| 21PTMs_Pmod | 21 PTMs | PTMs | 18 |
| 21PTMs_Rmod | 21 PTMs | PTMs | 18 |
| 21PTMs_Ymod | 21 PTMs | PTMs | 18 |
| human_multiprotease_ptm_argc | Multiprotease PTM | PTMs | 18 |
| human_multiprotease_ptm_aspn | Multiprotease PTM | PTMs | 18 |
| human_multiprotease_ptm_chymotrypsin | Multiprotease PTM | PTMs | 18 |
| human_multiprotease_ptm_gluc | Multiprotease PTM | PTMs | 18 |
| human_multiprotease_ptm_lysc | Multiprotease PTM | PTMs | 18 |
| human_multiprotease_ptm_trypsin | Multiprotease PTM | PTMs | 18 |
| human_phospho_Phos_SILAC | Phospho | PTMs | 18 |
| human_phospho_pY_SILAC | Phospho | PTMs | 18 |
| human_phospho_superSILAC | Phospho | PTMs | 18 |
| human_TMT | TMT | PTMs | 18 |
| PT_nonnatural | ProteomeTools | Synthetic | 18 |
| PT_orbitrap_HLAI | ProteomeTools | Synthetic | 18 |
| PT_orbitrap_HLAII | ProteomeTools | Synthetic | 18 |
| PT_orbitrap_HLAII_TMT | ProteomeTools | Synthetic | 18 |
| PT_orbitrap_HLAI_TMT | ProteomeTools | Synthetic | 18 |
| PT_orbitrap_aspn | ProteomeTools | Synthetic | 18 |
| PT_orbitrap_aspn_TMT | ProteomeTools | Synthetic | 18 |
| PT_orbitrap_lysn | ProteomeTools | Synthetic | 18 |
| PT_orbitrap_lysn_TMT | ProteomeTools | Synthetic | 18 |
| PT_orbitrap_tryptic_1 | ProteomeTools | Synthetic | 18 |
| PT_orbitrap_tryptic_2 | ProteomeTools | Synthetic | 18 |
| PT_orbitrap_tryptic_TMT | ProteomeTools | Synthetic | 18 |
| PT_timstof_HLAI | ProteomeTools | Synthetic | 18 |
| PT_timstof_HLAII | ProteomeTools | Synthetic | 18 |
| PT_timstof_aspn | ProteomeTools | Synthetic | 18 |
| PT_timstof_lysn | ProteomeTools | Synthetic | 18 |
| PT_timstof_tryptic | ProteomeTools | Synthetic | 18 |
Used by (1)
- A living proteomics benchmark for comprehensive evaluation of deep learning-based de novo peptide sequencing tools (2026) preprint as deposited
Methods on these papers (1)
- Living proteomics benchmark benchmark
Taken from the describing links only, so a paper that merely ran a tool on this data does not make that tool a method of it.