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	19
human_herceptin_chymotrypsin	Herceptin	Antibody	19
human_herceptin_gluc	Herceptin	Antibody	19
human_herceptin_lysc	Herceptin	Antibody	19
human_herceptin_lysn	Herceptin	Antibody	19
human_herceptin_trypsin	Herceptin	Antibody	19
human_mAb_aspn	mAb	Antibody	19
human_mAb_chymotrypsin	mAb	Antibody	19
human_mAb_trypsin	mAb	Antibody	19
mouse_mAb_aspn	mAb	Antibody	19
mouse_mAb_chymotrypsin	mAb	Antibody	19
mouse_mAb_trypsin	mAb	Antibody	19
human_multiprotease_aspn	Multiprotease	Digestion	19
human_multiprotease_chymotrypsin	Multiprotease	Digestion	19
human_multiprotease_gluc	Multiprotease	Digestion	19
human_multiprotease_lysc	Multiprotease	Digestion	19
human_multiprotease_lysn	Multiprotease	Digestion	19
human_multiprotease_trypsin	Multiprotease	Digestion	19
human_HLAI	Immunopeptidomics	HLA / MHC	19
human_HLAII	Immunopeptidomics	HLA / MHC	19
human_MHCI	Immunopeptidomics	HLA / MHC	19
mouse_MHCI	Immunopeptidomics	HLA / MHC	19
mouse_MHCII	Immunopeptidomics	HLA / MHC	19
human_agilent	Instrument	Instrument	19
human_astral	Instrument	Instrument	19
human_jurkat	Instrument	Instrument	19
staphylococcus_aureus_timstof	Instrument	Instrument	19
LFQ_orbitrap	LFQ	Instrument	19
LFQ_sciex	LFQ	Instrument	19
LFQ_timstof	LFQ	Instrument	19
multitool_orbitrap	Multitool	Instrument	19
multitool_sciex	Multitool	Instrument	19
9_species_apis_mellifera	9 species	Organism	19
9_species_bacillus_subtilis	9 species	Organism	19
9_species_candidatus_thiodiazotropha	9 species	Organism	19
9_species_human	9 species	Organism	19
9_species_methanosarcina_mazei	9 species	Organism	19
9_species_mus_musculus	9 species	Organism	19
9_species_saccharomyces_cerevisiae	9 species	Organism	19
9_species_solanum_lycopersicum	9 species	Organism	19
9_species_vigna_mungo	9 species	Organism	19
animal_invertebrate	Animal	Organism	19
animal_mammal_1	Animal	Organism	19
animal_mammal_2	Animal	Organism	19
CAMPI_F07	CAMPI	Organism	19
CAMPI_S11	CAMPI	Organism	19
fungus	Non-model organism	Organism	19
plant	Non-model organism	Organism	19
hela_single_cell	Single cell	Other	19
hela_single_cell_2	Single cell	Other	19
hela_single_cell_2_bulk	Single cell	Other	17
hela_single_cell_bulk	Single cell	Other	16
UPS	UPS	Other	19
iPRG	iPRG	Other	19
iPRG_2015	iPRG	Other	19
21PTMs_Kmod	21 PTMs	PTMs	19
21PTMs_Pmod	21 PTMs	PTMs	19
21PTMs_Rmod	21 PTMs	PTMs	19
21PTMs_Ymod	21 PTMs	PTMs	19
human_multiprotease_ptm_argc	Multiprotease PTM	PTMs	19
human_multiprotease_ptm_aspn	Multiprotease PTM	PTMs	19
human_multiprotease_ptm_chymotrypsin	Multiprotease PTM	PTMs	19
human_multiprotease_ptm_gluc	Multiprotease PTM	PTMs	19
human_multiprotease_ptm_lysc	Multiprotease PTM	PTMs	19
human_multiprotease_ptm_trypsin	Multiprotease PTM	PTMs	19
human_phospho_Phos_SILAC	Phospho	PTMs	19
human_phospho_pY_SILAC	Phospho	PTMs	19
human_phospho_superSILAC	Phospho	PTMs	19
human_TMT	TMT	PTMs	19
PT_nonnatural	ProteomeTools	Synthetic	19
PT_orbitrap_HLAI	ProteomeTools	Synthetic	19
PT_orbitrap_HLAII	ProteomeTools	Synthetic	19
PT_orbitrap_HLAII_TMT	ProteomeTools	Synthetic	19
PT_orbitrap_HLAI_TMT	ProteomeTools	Synthetic	19
PT_orbitrap_aspn	ProteomeTools	Synthetic	19
PT_orbitrap_aspn_TMT	ProteomeTools	Synthetic	19
PT_orbitrap_lysn	ProteomeTools	Synthetic	19
PT_orbitrap_lysn_TMT	ProteomeTools	Synthetic	19
PT_orbitrap_tryptic_1	ProteomeTools	Synthetic	19
PT_orbitrap_tryptic_2	ProteomeTools	Synthetic	19
PT_orbitrap_tryptic_TMT	ProteomeTools	Synthetic	19
PT_timstof_HLAI	ProteomeTools	Synthetic	19
PT_timstof_HLAII	ProteomeTools	Synthetic	19
PT_timstof_aspn	ProteomeTools	Synthetic	19
PT_timstof_lysn	ProteomeTools	Synthetic	19
PT_timstof_tryptic	ProteomeTools	Synthetic	19

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.

Seen in the charts

• The data underneath

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