Configuration

Prosit Transformer retrained on PROSPECT (PepSpecBench)

Prosit Transformer retrained by the PepSpecBench authors on the PROSPECT backbone-disjoint training split (500k spectra).

13 evaluations · 14 results

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Evaluations and results

13 evaluations · 14 results. Different protocols are not a single leaderboard.

Sorted by Spectral angle (median over spectra, shared canonical fragment space) (lower is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	Spectral angle (median over spectra, shared canonical fragment space)	Spectral angle similarity (median over spectra, shared canonical fragment space)	Pearson (median over spectra, shared canonical fragment space)	Spectral angle (median over spectra, shared canonical fragment space; four-decimal value with 95% bootstrap CI (Table 14))
Prosit Transformer retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench A. thaliana OOD subset, median SA, PepSpecBench A. thaliana OOD subset	0.102 (best in column)	Not reported	Not reported	Not reported
Prosit Transformer retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench PROSPECT-Mini test split, median SA, PepSpecBench PROSPECT-Mini test split	0.142	Not reported	Not reported	0.142
Prosit Transformer retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench C. elegans OOD subset, median SA, PepSpecBench C. elegans OOD subset	0.169	Not reported	Not reported	Not reported
Prosit Transformer retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench HeLa OOD subset, median SA, PepSpecBench HeLa OOD subset	0.259	Not reported	Not reported	Not reported
Prosit Transformer retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench Yeast OOD subset, median SA, PepSpecBench Yeast OOD subset	0.288	Not reported	Not reported	Not reported
Prosit Transformer retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench E. coli OOD subsets (both sources aggregated), median SA, PepSpecBench E. coli OOD subsets (both sources aggregated)	0.298	Not reported	Not reported	Not reported
Prosit Transformer retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench A. thaliana OOD subset, median SAS, PepSpecBench A. thaliana OOD subset	Not reported	0.898 (best in column)	Not reported	Not reported
Prosit Transformer retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench C. elegans OOD subset, median SAS, PepSpecBench C. elegans OOD subset	Not reported	0.831	Not reported	Not reported
Prosit Transformer retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench E. coli OOD subsets (both sources aggregated), median SAS, PepSpecBench E. coli OOD subsets (both sources aggregated)	Not reported	0.702	Not reported	Not reported
Prosit Transformer retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench HeLa OOD subset, median SAS, PepSpecBench HeLa OOD subset	Not reported	0.741	Not reported	Not reported
Prosit Transformer retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench PROSPECT-Mini test split, median PCC, PepSpecBench PROSPECT-Mini test split	Not reported	Not reported	0.885	Not reported
Prosit Transformer retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench PROSPECT-Mini test split, median SAS, PepSpecBench PROSPECT-Mini test split	Not reported	0.858	Not reported	Not reported
Prosit Transformer retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench Yeast OOD subset, median SAS, PepSpecBench Yeast OOD subset	Not reported	0.712	Not reported	Not reported

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Prosit Transformer retrained on PROSPECT (PepSpecBench)	Protocol: PepSpecBench A. thaliana OOD subset, median SA Dataset: PepSpecBench A. thaliana OOD subset	0.102 Spectral angle (median over spectra, shared canonical fragment space) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Prosit Transformer (trained on PROSPECT) on A. thaliana OOD subset, SA lit-otheromics-20261011-pepspecbench-protocol-a-thaliana-sa Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 4, block 'PROSPECT Trained', row 'Prosit Tran.', column 'A. thaliana' (first value of SA / SAS)
Configuration: Prosit Transformer retrained on PROSPECT (PepSpecBench)	Protocol: PepSpecBench A. thaliana OOD subset, median SAS Dataset: PepSpecBench A. thaliana OOD subset	0.898 Spectral angle similarity (median over spectra, shared canonical fragment space) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Prosit Transformer (trained on PROSPECT) on A. thaliana OOD subset, SAS lit-otheromics-20261011-pepspecbench-protocol-a-thaliana-sas Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 4, block 'PROSPECT Trained', row 'Prosit Tran.', column 'A. thaliana' (second value of SA / SAS)
Configuration: Prosit Transformer retrained on PROSPECT (PepSpecBench)	Protocol: PepSpecBench C. elegans OOD subset, median SA Dataset: PepSpecBench C. elegans OOD subset	0.169 Spectral angle (median over spectra, shared canonical fragment space) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Prosit Transformer (trained on PROSPECT) on C. elegans OOD subset, SA lit-otheromics-20261011-pepspecbench-protocol-c-elegans-sa Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 4, block 'PROSPECT Trained', row 'Prosit Tran.', column 'C. elegans' (first value of SA / SAS)
Configuration: Prosit Transformer retrained on PROSPECT (PepSpecBench)	Protocol: PepSpecBench C. elegans OOD subset, median SAS Dataset: PepSpecBench C. elegans OOD subset	0.831 Spectral angle similarity (median over spectra, shared canonical fragment space) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Prosit Transformer (trained on PROSPECT) on C. elegans OOD subset, SAS lit-otheromics-20261011-pepspecbench-protocol-c-elegans-sas Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 4, block 'PROSPECT Trained', row 'Prosit Tran.', column 'C. elegans' (second value of SA / SAS)
Configuration: Prosit Transformer retrained on PROSPECT (PepSpecBench)	Protocol: PepSpecBench E. coli OOD subsets (both sources aggregated), median SA Dataset: PepSpecBench E. coli OOD subsets (both sources aggregated)	0.298 Spectral angle (median over spectra, shared canonical fragment space) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Prosit Transformer (trained on PROSPECT) on E. coli OOD subsets (both sources aggregated), SA lit-otheromics-20261011-pepspecbench-protocol-e-coli-sa Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 4, block 'PROSPECT Trained', row 'Prosit Tran.', column 'E. coli' (first value of SA / SAS)
Configuration: Prosit Transformer retrained on PROSPECT (PepSpecBench)	Protocol: PepSpecBench E. coli OOD subsets (both sources aggregated), median SAS Dataset: PepSpecBench E. coli OOD subsets (both sources aggregated)	0.702 Spectral angle similarity (median over spectra, shared canonical fragment space) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Prosit Transformer (trained on PROSPECT) on E. coli OOD subsets (both sources aggregated), SAS lit-otheromics-20261011-pepspecbench-protocol-e-coli-sas Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 4, block 'PROSPECT Trained', row 'Prosit Tran.', column 'E. coli' (second value of SA / SAS)
Configuration: Prosit Transformer retrained on PROSPECT (PepSpecBench)	Protocol: PepSpecBench HeLa OOD subset, median SA Dataset: PepSpecBench HeLa OOD subset	0.259 Spectral angle (median over spectra, shared canonical fragment space) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Prosit Transformer (trained on PROSPECT) on HeLa OOD subset, SA lit-otheromics-20261011-pepspecbench-protocol-hela-sa Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 4, block 'PROSPECT Trained', row 'Prosit Tran.', column 'HeLa' (first value of SA / SAS)
Configuration: Prosit Transformer retrained on PROSPECT (PepSpecBench)	Protocol: PepSpecBench HeLa OOD subset, median SAS Dataset: PepSpecBench HeLa OOD subset	0.741 Spectral angle similarity (median over spectra, shared canonical fragment space) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Prosit Transformer (trained on PROSPECT) on HeLa OOD subset, SAS lit-otheromics-20261011-pepspecbench-protocol-hela-sas Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 4, block 'PROSPECT Trained', row 'Prosit Tran.', column 'HeLa' (second value of SA / SAS)
Configuration: Prosit Transformer retrained on PROSPECT (PepSpecBench)	Protocol: PepSpecBench PROSPECT-Mini test split, median PCC Dataset: PepSpecBench PROSPECT-Mini test split	0.885 Pearson (median over spectra, shared canonical fragment space) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Prosit Transformer (trained on PROSPECT) on PROSPECT-Mini test split, PCC lit-otheromics-20261011-pepspecbench-protocol-prospect-pcc Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 2, row 'Prosit Trans.', column group 'PROSPECT', column 'PCC'
Configuration: Prosit Transformer retrained on PROSPECT (PepSpecBench)	Protocol: PepSpecBench PROSPECT-Mini test split, median SA Dataset: PepSpecBench PROSPECT-Mini test split	0.142 Spectral angle (median over spectra, shared canonical fragment space; four-decimal value with 95% bootstrap CI (Table 14)) unitless · lower Uncertainty: 95% CI 0.1396 to 0.1444. Table 14 caption: 95% bootstrap CI, 1000 resamples over 50k test spectra. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Prosit Transformer (trained on PROSPECT) on PROSPECT-Mini test split, SA lit-otheromics-20261011-pepspecbench-protocol-prospect-sa Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 14, source 'PROSPECT', row 'Prosit Trans.', column 'Med. SA'
Configuration: Prosit Transformer retrained on PROSPECT (PepSpecBench)	Protocol: PepSpecBench PROSPECT-Mini test split, median SA Dataset: PepSpecBench PROSPECT-Mini test split	0.142 Spectral angle (median over spectra, shared canonical fragment space) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Prosit Transformer (trained on PROSPECT) on PROSPECT-Mini test split, SA lit-otheromics-20261011-pepspecbench-protocol-prospect-sa Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 2, row 'Prosit Trans.', column group 'PROSPECT', column 'SA'
Configuration: Prosit Transformer retrained on PROSPECT (PepSpecBench)	Protocol: PepSpecBench PROSPECT-Mini test split, median SAS Dataset: PepSpecBench PROSPECT-Mini test split	0.858 Spectral angle similarity (median over spectra, shared canonical fragment space) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Prosit Transformer (trained on PROSPECT) on PROSPECT-Mini test split, SAS lit-otheromics-20261011-pepspecbench-protocol-prospect-sas Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 2, row 'Prosit Trans.', column group 'PROSPECT', column 'SAS'
Configuration: Prosit Transformer retrained on PROSPECT (PepSpecBench)	Protocol: PepSpecBench Yeast OOD subset, median SA Dataset: PepSpecBench Yeast OOD subset	0.288 Spectral angle (median over spectra, shared canonical fragment space) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Prosit Transformer (trained on PROSPECT) on Yeast OOD subset, SA lit-otheromics-20261011-pepspecbench-protocol-yeast-sa Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 4, block 'PROSPECT Trained', row 'Prosit Tran.', column 'Yeast' (first value of SA / SAS)
Configuration: Prosit Transformer retrained on PROSPECT (PepSpecBench)	Protocol: PepSpecBench Yeast OOD subset, median SAS Dataset: PepSpecBench Yeast OOD subset	0.712 Spectral angle similarity (median over spectra, shared canonical fragment space) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Prosit Transformer (trained on PROSPECT) on Yeast OOD subset, SAS lit-otheromics-20261011-pepspecbench-protocol-yeast-sas Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 4, block 'PROSPECT Trained', row 'Prosit Tran.', column 'Yeast' (second value of SA / SAS)

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PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Original source · arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering

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Technical metadata and extraction receipts

Stable ID: lit-otheromics-20261011-pepspecbench-config-prosit-transformer-trained-prospect

areas: proteins-complexes
contexts: research
method types: supervised_machine_learning
reported name: Prosit Trans.
foundation model eligible: false
parameters: Retrained on the PROSPECT-Mini backbone-disjoint training split (500k/50k/50k train/validation/test); outputs projected to the shared canonical b/y fragment space; hyperparameters in Appendix Table 12
training setting: Trained on PROSPECT
access reuse: Benchmark data at https://huggingface.co/datasets/Chris-young-2004/PepSpecBench; model code not stated
source locator: Section 3.2; Appendix E and Table 12
missing metadata: version: reason: unreported; note: No model or code version is printed

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