PepSpecBench PROSPECT-Mini test split, median SAS; PepSpecBench v1

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6 recorded evaluations, 6 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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All evaluations

6 evaluations · 6 results. Different protocols are not a single leaderboard.

Protocol: PepSpecBench PROSPECT-Mini test split, median SAS · Dataset: PepSpecBench PROSPECT-Mini test split

Sorted by Spectral angle similarity (median over spectra, shared canonical fragment space) (higher 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	Spectral angle similarity (median over spectra, shared canonical fragment space)
Prosit retrained on PROSPECT (PepSpecBench)Evaluation	0.862 (best in column)
Prosit Transformer retrained on PROSPECT (PepSpecBench)Evaluation	0.858
UniSpec retrained on PROSPECT (PepSpecBench)Evaluation	0.807
PredFull retrained on PROSPECT (PepSpecBench)Evaluation	0.797
AlphaPeptDeep retrained on PROSPECT (PepSpecBench)Evaluation	0.722
FastSpel retrained on PROSPECT (PepSpecBench)Evaluation	0.621

All 6 result rows with coverage, uncertainty and sources

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
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 checked Methods, coverage and source AlphaPeptDeep (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 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 checked Methods, coverage and source FastSpel (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 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 checked Methods, coverage and source PredFull (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 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 checked Methods, coverage and source Prosit (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 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: 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 checked Methods, coverage and source UniSpec (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'

Source checking is not independent reproduction. Release 2026-10-23-5347695500ed.

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External evaluations: 6

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Sources and history

Release 2026-10-23-5347695500ed · Record review: source checked

1 source record and release history

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-protocol-prospect-sas

areas: proteins-complexes
contexts: research
protocol: Predict fragment intensities for each spectrum, project to the shared canonical b/y space, mask invalid positions, compute SAS per spectrum and take the median.
version: PepSpecBench v1
metric: spectral-angle-similarity
metric direction: higher
unit: unitless
metric qualifier: median over spectra, shared canonical fragment space
source locator: Section 3.3 (metrics and evaluation protocol); Table 2
limitations: Preprint.; Medians, not means.

Related records

part of: PepSpecBench
uses data: PepSpecBench PROSPECT-Mini test split
assessment: AlphaPeptDeep (trained on PROSPECT) on PROSPECT-Mini test split, SAS
assessment: FastSpel (trained on PROSPECT) on PROSPECT-Mini test split, SAS
assessment: PredFull (trained on PROSPECT) on PROSPECT-Mini test split, SAS
assessment: Prosit (trained on PROSPECT) on PROSPECT-Mini test split, SAS
assessment: Prosit Transformer (trained on PROSPECT) on PROSPECT-Mini test split, SAS
assessment: UniSpec (trained on PROSPECT) on PROSPECT-Mini test split, SAS