Human HeLa cancer cell spectra from PXD027742 (20k), an intra-species domain shift.
24 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 MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench HeLa OOD subset, median SA Dataset: PepSpecBench HeLa OOD subset | 0.468 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 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 'MassIVE-KB Trained', row 'AlphaPep.', column 'HeLa' (first value of SA / SAS) |
| Configuration: AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench HeLa OOD subset, median SAS Dataset: PepSpecBench HeLa OOD subset | 0.532 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 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 'MassIVE-KB Trained', row 'AlphaPep.', column 'HeLa' (second value of SA / SAS) |
| Configuration: AlphaPeptDeep retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench HeLa OOD subset, median SA Dataset: PepSpecBench HeLa OOD subset | 0.274 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 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 'AlphaPep.', column 'HeLa' (first value of SA / SAS) |
| Configuration: AlphaPeptDeep retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench HeLa OOD subset, median SAS Dataset: PepSpecBench HeLa OOD subset | 0.726 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 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 'AlphaPep.', column 'HeLa' (second value of SA / SAS) |
| Configuration: FastSpel retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench HeLa OOD subset, median SA Dataset: PepSpecBench HeLa OOD subset | 0.461 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 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 'MassIVE-KB Trained', row 'FastSpel', column 'HeLa' (first value of SA / SAS) |
| Configuration: FastSpel retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench HeLa OOD subset, median SAS Dataset: PepSpecBench HeLa OOD subset | 0.539 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 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 'MassIVE-KB Trained', row 'FastSpel', column 'HeLa' (second value of SA / SAS) |
| Configuration: FastSpel retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench HeLa OOD subset, median SA Dataset: PepSpecBench HeLa OOD subset | 0.361 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 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 'FastSpel', column 'HeLa' (first value of SA / SAS) |
| Configuration: FastSpel retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench HeLa OOD subset, median SAS Dataset: PepSpecBench HeLa OOD subset | 0.639 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 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 'FastSpel', column 'HeLa' (second value of SA / SAS) |
| Configuration: PredFull retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench HeLa OOD subset, median SA Dataset: PepSpecBench HeLa OOD subset | 0.22 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 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 'MassIVE-KB Trained', row 'PredFull', column 'HeLa' (first value of SA / SAS) |
| Configuration: PredFull retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench HeLa OOD subset, median SAS Dataset: PepSpecBench HeLa OOD subset | 0.78 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 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 'MassIVE-KB Trained', row 'PredFull', column 'HeLa' (second value of SA / SAS) |
| Configuration: PredFull retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench HeLa OOD subset, median SA Dataset: PepSpecBench HeLa OOD subset | 0.196 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 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 'PredFull', column 'HeLa' (first value of SA / SAS) |
| Configuration: PredFull retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench HeLa OOD subset, median SAS Dataset: PepSpecBench HeLa OOD subset | 0.804 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 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 'PredFull', column 'HeLa' (second value of SA / SAS) |
| Configuration: Prosit retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench HeLa OOD subset, median SA Dataset: PepSpecBench HeLa OOD subset | 0.471 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 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 'MassIVE-KB Trained', row 'Prosit', column 'HeLa' (first value of SA / SAS) |
| Configuration: Prosit retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench HeLa OOD subset, median SAS Dataset: PepSpecBench HeLa OOD subset | 0.529 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 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 'MassIVE-KB Trained', row 'Prosit', column 'HeLa' (second value of SA / SAS) |
| Configuration: Prosit retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench HeLa OOD subset, median SA Dataset: PepSpecBench HeLa OOD subset | 0.244 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 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', column 'HeLa' (first value of SA / SAS) |
| Configuration: Prosit retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench HeLa OOD subset, median SAS Dataset: PepSpecBench HeLa OOD subset | 0.756 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 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', column 'HeLa' (second value of SA / SAS) |
| Configuration: Prosit Transformer retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench HeLa OOD subset, median SA Dataset: PepSpecBench HeLa OOD subset | 0.475 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 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 'MassIVE-KB Trained', row 'Prosit Tran.', column 'HeLa' (first value of SA / SAS) |
| Configuration: Prosit Transformer retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench HeLa OOD subset, median SAS Dataset: PepSpecBench HeLa OOD subset | 0.525 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 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 'MassIVE-KB Trained', row 'Prosit Tran.', column 'HeLa' (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 checkedMethods, coverage and sourceProsit 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 checkedMethods, coverage and sourceProsit 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: UniSpec retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench HeLa OOD subset, median SA Dataset: PepSpecBench HeLa OOD subset | 0.38 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 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 'MassIVE-KB Trained', row 'UniSpec', column 'HeLa' (first value of SA / SAS) |
| Configuration: UniSpec retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench HeLa OOD subset, median SAS Dataset: PepSpecBench HeLa OOD subset | 0.62 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 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 'MassIVE-KB Trained', row 'UniSpec', column 'HeLa' (second value of SA / SAS) |
| Configuration: UniSpec retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench HeLa OOD subset, median SA Dataset: PepSpecBench HeLa OOD subset | 0.251 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 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 'UniSpec', column 'HeLa' (first value of SA / SAS) |
| Configuration: UniSpec retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench HeLa OOD subset, median SAS Dataset: PepSpecBench HeLa OOD subset | 0.749 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 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 'UniSpec', column 'HeLa' (second value of SA / 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 Out-of-distribution evaluation (zero-shot) 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 Human HeLa cancer cell spectra from PXD027742 (20k), an intra-species domain shift. 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 HeLa OOD subset 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-hela