PepSpecBench PROSPECT-Mini test split, median PCC; 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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Results

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All evaluations

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

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

Sorted by Pearson (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	Pearson (median over spectra, shared canonical fragment space)
Prosit retrained on PROSPECT (PepSpecBench)Evaluation	0.892 (best in column)
Prosit Transformer retrained on PROSPECT (PepSpecBench)Evaluation	0.885
UniSpec retrained on PROSPECT (PepSpecBench)Evaluation	0.794
PredFull retrained on PROSPECT (PepSpecBench)Evaluation	0.749
AlphaPeptDeep retrained on PROSPECT (PepSpecBench)Evaluation	0.593
FastSpel retrained on PROSPECT (PepSpecBench)Evaluation	0.015

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 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 checked Methods, coverage and source AlphaPeptDeep (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: 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 checked Methods, coverage and source FastSpel (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: 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 checked Methods, coverage and source PredFull (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: 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 checked Methods, coverage and source Prosit (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 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: 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 checked Methods, coverage and source UniSpec (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'

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

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Recorded evaluations

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External evaluations: 6

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Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

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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-pcc

areas: proteins-complexes
contexts: research
protocol: Predict fragment intensities for each spectrum, project to the shared canonical b/y space, mask invalid positions, compute PCC per spectrum and take the median.
version: PepSpecBench v1
metric: pearson-correlation
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, PCC
assessment: FastSpel (trained on PROSPECT) on PROSPECT-Mini test split, PCC
assessment: PredFull (trained on PROSPECT) on PROSPECT-Mini test split, PCC
assessment: Prosit (trained on PROSPECT) on PROSPECT-Mini test split, PCC
assessment: Prosit Transformer (trained on PROSPECT) on PROSPECT-Mini test split, PCC
assessment: UniSpec (trained on PROSPECT) on PROSPECT-Mini test split, PCC