PROSPECT (ProteomeTools) 50k test spectra, backbone-disjoint from training; 50% unmodified and 50% PTM.
18 evaluations · 24 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: AlphaPeptDeep retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench PROSPECT-Mini test split, median PCC Dataset: PepSpecBench PROSPECT-Mini test split | 0.593 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 checkedMethods, coverage and sourceAlphaPeptDeep (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 'AlphaPeptDeep', column group 'PROSPECT', column 'PCC' |
| Configuration: AlphaPeptDeep retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench PROSPECT-Mini test split, median SA Dataset: PepSpecBench PROSPECT-Mini test split | 0.278 Spectral angle (median over spectra, shared canonical fragment space; four-decimal value with 95% bootstrap CI (Table 14)) unitless · lower Uncertainty: 95% CI 0.2759 to 0.2803. Table 14 caption: 95% bootstrap CI, 1000 resamples over 50k test spectra. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaPeptDeep (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 'AlphaPeptDeep', column 'Med. SA' |
| Configuration: AlphaPeptDeep retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench PROSPECT-Mini test split, median SA Dataset: PepSpecBench PROSPECT-Mini test split | 0.278 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 checkedMethods, coverage and sourceAlphaPeptDeep (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 'AlphaPeptDeep', column group 'PROSPECT', column 'SA' |
| Configuration: AlphaPeptDeep retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench PROSPECT-Mini test split, median SAS Dataset: PepSpecBench PROSPECT-Mini test split | 0.722 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 checkedMethods, coverage and sourceAlphaPeptDeep (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 'AlphaPeptDeep', column group 'PROSPECT', column 'SAS' |
| Configuration: FastSpel retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench PROSPECT-Mini test split, median PCC Dataset: PepSpecBench PROSPECT-Mini test split | 0.015 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 checkedMethods, coverage and sourceFastSpel (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 'FastSpel', column group 'PROSPECT', column 'PCC' |
| Configuration: FastSpel retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench PROSPECT-Mini test split, median SA Dataset: PepSpecBench PROSPECT-Mini test split | 0.379 Spectral angle (median over spectra, shared canonical fragment space; four-decimal value with 95% bootstrap CI (Table 14)) unitless · lower Uncertainty: 95% CI 0.3783 to 0.3801. Table 14 caption: 95% bootstrap CI, 1000 resamples over 50k test spectra. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceFastSpel (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 'FastSpel', column 'Med. SA' |
| Configuration: FastSpel retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench PROSPECT-Mini test split, median SA Dataset: PepSpecBench PROSPECT-Mini test split | 0.379 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 checkedMethods, coverage and sourceFastSpel (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 'FastSpel', column group 'PROSPECT', column 'SA' |
| Configuration: FastSpel retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench PROSPECT-Mini test split, median SAS Dataset: PepSpecBench PROSPECT-Mini test split | 0.621 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 checkedMethods, coverage and sourceFastSpel (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 'FastSpel', column group 'PROSPECT', column 'SAS' |
| Configuration: PredFull retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench PROSPECT-Mini test split, median PCC Dataset: PepSpecBench PROSPECT-Mini test split | 0.749 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 checkedMethods, coverage and sourcePredFull (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 'PredFull', column group 'PROSPECT', column 'PCC' |
| Configuration: PredFull retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench PROSPECT-Mini test split, median SA Dataset: PepSpecBench PROSPECT-Mini test split | 0.203 Spectral angle (median over spectra, shared canonical fragment space; four-decimal value with 95% bootstrap CI (Table 14)) unitless · lower Uncertainty: 95% CI 0.2022 to 0.2049. Table 14 caption: 95% bootstrap CI, 1000 resamples over 50k test spectra. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcePredFull (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 'PredFull', column 'Med. SA' |
| Configuration: PredFull retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench PROSPECT-Mini test split, median SA Dataset: PepSpecBench PROSPECT-Mini test split | 0.204 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 checkedMethods, coverage and sourcePredFull (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 'PredFull', column group 'PROSPECT', column 'SA' |
| Configuration: PredFull retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench PROSPECT-Mini test split, median SAS Dataset: PepSpecBench PROSPECT-Mini test split | 0.797 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 checkedMethods, coverage and sourcePredFull (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 'PredFull', column group 'PROSPECT', column 'SAS' |
| Configuration: Prosit retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench PROSPECT-Mini test split, median PCC Dataset: PepSpecBench PROSPECT-Mini test split | 0.892 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 checkedMethods, coverage and sourceProsit (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', column group 'PROSPECT', column 'PCC' |
| Configuration: Prosit retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench PROSPECT-Mini test split, median SA Dataset: PepSpecBench PROSPECT-Mini test split | 0.138 Spectral angle (median over spectra, shared canonical fragment space; four-decimal value with 95% bootstrap CI (Table 14)) unitless · lower Uncertainty: 95% CI 0.1354 to 0.1397. Table 14 caption: 95% bootstrap CI, 1000 resamples over 50k test spectra. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceProsit (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', column 'Med. SA' |
| Configuration: Prosit retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench PROSPECT-Mini test split, median SA Dataset: PepSpecBench PROSPECT-Mini test split | 0.138 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 checkedMethods, coverage and sourceProsit (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', column group 'PROSPECT', column 'SA' |
| Configuration: Prosit retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench PROSPECT-Mini test split, median SAS Dataset: PepSpecBench PROSPECT-Mini test split | 0.862 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 checkedMethods, coverage and sourceProsit (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', column group 'PROSPECT', column '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 checkedMethods, coverage and sourceProsit 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 checkedMethods, coverage and sourceProsit 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 checkedMethods, coverage and sourceProsit 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 checkedMethods, coverage and sourceProsit 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: UniSpec retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench PROSPECT-Mini test split, median PCC Dataset: PepSpecBench PROSPECT-Mini test split | 0.794 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 checkedMethods, coverage and sourceUniSpec (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 'UniSpec', column group 'PROSPECT', column 'PCC' |
| Configuration: UniSpec retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench PROSPECT-Mini test split, median SA Dataset: PepSpecBench PROSPECT-Mini test split | 0.193 Spectral angle (median over spectra, shared canonical fragment space; four-decimal value with 95% bootstrap CI (Table 14)) unitless · lower Uncertainty: 95% CI 0.1912 to 0.1951. Table 14 caption: 95% bootstrap CI, 1000 resamples over 50k test spectra. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceUniSpec (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 'UniSpec', column 'Med. SA' |
| Configuration: UniSpec retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench PROSPECT-Mini test split, median SA Dataset: PepSpecBench PROSPECT-Mini test split | 0.193 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 checkedMethods, coverage and sourceUniSpec (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 'UniSpec', column group 'PROSPECT', column 'SA' |
| Configuration: UniSpec retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench PROSPECT-Mini test split, median SAS Dataset: PepSpecBench PROSPECT-Mini test split | 0.807 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 checkedMethods, coverage and sourceUniSpec (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 'UniSpec', column group 'PROSPECT', column 'SAS' |
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| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Source location Table 1; Appendix C.1 and C.6 Context-only references | PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction Table 1; Appendix C.1 and C.6 Version: arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Split Test Context-only references | PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction Table 1; Appendix C.1 and C.6 Version: arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Version PepSpecBench v1 Context-only references | PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction Table 1; Appendix C.1 and C.6 Version: arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Description PROSPECT (ProteomeTools) 50k test spectra, backbone-disjoint from training; 50% unmodified and 50% PTM. Context-only references | PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction Table 1; Appendix C.1 and C.6 Version: arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Name PepSpecBench PROSPECT-Mini test split Context-only references | PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction Table 1; Appendix C.1 and C.6 Version: arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-10-23-5347695500ed · Record review: source checked
Stable ID: lit-otheromics-20261011-pepspecbench-data-prospect