| Configuration: AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median PCC Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.915 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 MassIVE-KB) on MassIVE-KB-Mini test split, PCC lit-otheromics-20261011-pepspecbench-protocol-massive-kb-pcc Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 2, row 'AlphaPeptDeep', column group 'MassIVE-KB', column 'PCC' |
|---|
| Configuration: AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median SA Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.129 Spectral angle (median over spectra, shared canonical fragment space; four-decimal value with 95% bootstrap CI (Table 14)) unitless · lower Uncertainty: 95% CI 0.1277 to 0.1300. 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 MassIVE-KB) on MassIVE-KB-Mini test split, SA lit-otheromics-20261011-pepspecbench-protocol-massive-kb-sa Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 14, source 'MassIVE-KB', row 'AlphaPeptDeep', column 'Med. SA' |
|---|
| Configuration: AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median SA Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.129 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 MassIVE-KB) on MassIVE-KB-Mini test split, SA lit-otheromics-20261011-pepspecbench-protocol-massive-kb-sa Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 2, row 'AlphaPeptDeep', column group 'MassIVE-KB', column 'SA' |
|---|
| Configuration: AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median SAS Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.871 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 MassIVE-KB) on MassIVE-KB-Mini test split, SAS lit-otheromics-20261011-pepspecbench-protocol-massive-kb-sas Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 2, row 'AlphaPeptDeep', column group 'MassIVE-KB', column 'SAS' |
|---|
| Configuration: FastSpel retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median PCC Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.01 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 MassIVE-KB) on MassIVE-KB-Mini test split, PCC lit-otheromics-20261011-pepspecbench-protocol-massive-kb-pcc Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 2, row 'FastSpel', column group 'MassIVE-KB', column 'PCC' |
|---|
| Configuration: FastSpel retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median SA Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.476 Spectral angle (median over spectra, shared canonical fragment space; four-decimal value with 95% bootstrap CI (Table 14)) unitless · lower Uncertainty: 95% CI 0.4752 to 0.4762. 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 MassIVE-KB) on MassIVE-KB-Mini test split, SA lit-otheromics-20261011-pepspecbench-protocol-massive-kb-sa Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 14, source 'MassIVE-KB', row 'FastSpel', column 'Med. SA' |
|---|
| Configuration: FastSpel retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median SA Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.476 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 MassIVE-KB) on MassIVE-KB-Mini test split, SA lit-otheromics-20261011-pepspecbench-protocol-massive-kb-sa Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 2, row 'FastSpel', column group 'MassIVE-KB', column 'SA' |
|---|
| Configuration: FastSpel retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median SAS Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.524 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 MassIVE-KB) on MassIVE-KB-Mini test split, SAS lit-otheromics-20261011-pepspecbench-protocol-massive-kb-sas Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 2, row 'FastSpel', column group 'MassIVE-KB', column 'SAS' |
|---|
| Configuration: PredFull retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median PCC Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.83 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 MassIVE-KB) on MassIVE-KB-Mini test split, PCC lit-otheromics-20261011-pepspecbench-protocol-massive-kb-pcc Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 2, row 'PredFull', column group 'MassIVE-KB', column 'PCC' |
|---|
| Configuration: PredFull retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median SA Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.167 Spectral angle (median over spectra, shared canonical fragment space; four-decimal value with 95% bootstrap CI (Table 14)) unitless · lower Uncertainty: 95% CI 0.1666 to 0.1680. 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 MassIVE-KB) on MassIVE-KB-Mini test split, SA lit-otheromics-20261011-pepspecbench-protocol-massive-kb-sa Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 14, source 'MassIVE-KB', row 'PredFull', column 'Med. SA' |
|---|
| Configuration: PredFull retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median SA Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.167 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 MassIVE-KB) on MassIVE-KB-Mini test split, SA lit-otheromics-20261011-pepspecbench-protocol-massive-kb-sa Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 2, row 'PredFull', column group 'MassIVE-KB', column 'SA' |
|---|
| Configuration: PredFull retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median SAS Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.833 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 MassIVE-KB) on MassIVE-KB-Mini test split, SAS lit-otheromics-20261011-pepspecbench-protocol-massive-kb-sas Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 2, row 'PredFull', column group 'MassIVE-KB', column 'SAS' |
|---|
| Configuration: Prosit retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median PCC Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.949 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 MassIVE-KB) on MassIVE-KB-Mini test split, PCC lit-otheromics-20261011-pepspecbench-protocol-massive-kb-pcc Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 2, row 'Prosit', column group 'MassIVE-KB', column 'PCC' |
|---|
| Configuration: Prosit retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median SA Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.0995 Spectral angle (median over spectra, shared canonical fragment space; four-decimal value with 95% bootstrap CI (Table 14)) unitless · lower Uncertainty: 95% CI 0.0984 to 0.1006. 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 MassIVE-KB) on MassIVE-KB-Mini test split, SA lit-otheromics-20261011-pepspecbench-protocol-massive-kb-sa Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 14, source 'MassIVE-KB', row 'Prosit', column 'Med. SA' |
|---|
| Configuration: Prosit retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median SA Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.1 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 MassIVE-KB) on MassIVE-KB-Mini test split, SA lit-otheromics-20261011-pepspecbench-protocol-massive-kb-sa Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 2, row 'Prosit', column group 'MassIVE-KB', column 'SA' |
|---|
| Configuration: Prosit retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median SAS Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.901 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 MassIVE-KB) on MassIVE-KB-Mini test split, SAS lit-otheromics-20261011-pepspecbench-protocol-massive-kb-sas Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 2, row 'Prosit', column group 'MassIVE-KB', column 'SAS' |
|---|
| Configuration: Prosit Transformer retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median PCC Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.951 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 MassIVE-KB) on MassIVE-KB-Mini test split, PCC lit-otheromics-20261011-pepspecbench-protocol-massive-kb-pcc Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 2, row 'Prosit Trans.', column group 'MassIVE-KB', column 'PCC' |
|---|
| Configuration: Prosit Transformer retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median SA Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.0977 Spectral angle (median over spectra, shared canonical fragment space; four-decimal value with 95% bootstrap CI (Table 14)) unitless · lower Uncertainty: 95% CI 0.0969 to 0.0986. 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 MassIVE-KB) on MassIVE-KB-Mini test split, SA lit-otheromics-20261011-pepspecbench-protocol-massive-kb-sa Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 14, source 'MassIVE-KB', row 'Prosit Trans.', column 'Med. SA' |
|---|
| Configuration: Prosit Transformer retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median SA Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.098 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 MassIVE-KB) on MassIVE-KB-Mini test split, SA lit-otheromics-20261011-pepspecbench-protocol-massive-kb-sa Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 2, row 'Prosit Trans.', column group 'MassIVE-KB', column 'SA' |
|---|
| Configuration: Prosit Transformer retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median SAS Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.902 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 MassIVE-KB) on MassIVE-KB-Mini test split, SAS lit-otheromics-20261011-pepspecbench-protocol-massive-kb-sas Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 2, row 'Prosit Trans.', column group 'MassIVE-KB', column 'SAS' |
|---|
| Configuration: UniSpec retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median PCC Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.048 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 MassIVE-KB) on MassIVE-KB-Mini test split, PCC lit-otheromics-20261011-pepspecbench-protocol-massive-kb-pcc Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 2, row 'UniSpec', column group 'MassIVE-KB', column 'PCC' |
|---|
| Configuration: UniSpec retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median SA Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.337 Spectral angle (median over spectra, shared canonical fragment space; four-decimal value with 95% bootstrap CI (Table 14)) unitless · lower Uncertainty: 95% CI 0.3365 to 0.3374. 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 MassIVE-KB) on MassIVE-KB-Mini test split, SA lit-otheromics-20261011-pepspecbench-protocol-massive-kb-sa Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 14, source 'MassIVE-KB', row 'UniSpec', column 'Med. SA' |
|---|
| Configuration: UniSpec retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median SA Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.337 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 MassIVE-KB) on MassIVE-KB-Mini test split, SA lit-otheromics-20261011-pepspecbench-protocol-massive-kb-sa Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 2, row 'UniSpec', column group 'MassIVE-KB', column 'SA' |
|---|
| Configuration: UniSpec retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench MassIVE-KB-Mini test split, median SAS Dataset: PepSpecBench MassIVE-KB-Mini test split | 0.663 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 MassIVE-KB) on MassIVE-KB-Mini test split, SAS lit-otheromics-20261011-pepspecbench-protocol-massive-kb-sas Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 2, row 'UniSpec', column group 'MassIVE-KB', column 'SAS' |
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