Configuration

UniSpec retrained on PROSPECT (PepSpecBench)

UniSpec retrained by the PepSpecBench authors on the PROSPECT backbone-disjoint training split (500k spectra).

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Evaluations and results

13 evaluations · 14 results. Different protocols are not a single leaderboard.

Sorted by Spectral angle (median over spectra, shared canonical fragment space) (lower 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	Protocol and dataset	Spectral angle (median over spectra, shared canonical fragment space)	Spectral angle similarity (median over spectra, shared canonical fragment space)	Pearson (median over spectra, shared canonical fragment space)	Spectral angle (median over spectra, shared canonical fragment space; four-decimal value with 95% bootstrap CI (Table 14))
UniSpec retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench A. thaliana OOD subset, median SA, PepSpecBench A. thaliana OOD subset	0.12 (best in column)	Not reported	Not reported	Not reported
UniSpec retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench C. elegans OOD subset, median SA, PepSpecBench C. elegans OOD subset	0.188	Not reported	Not reported	Not reported
UniSpec retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench PROSPECT-Mini test split, median SA, PepSpecBench PROSPECT-Mini test split	0.193	Not reported	Not reported	0.193
UniSpec retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench HeLa OOD subset, median SA, PepSpecBench HeLa OOD subset	0.251	Not reported	Not reported	Not reported
UniSpec retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench Yeast OOD subset, median SA, PepSpecBench Yeast OOD subset	0.294	Not reported	Not reported	Not reported
UniSpec retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench E. coli OOD subsets (both sources aggregated), median SA, PepSpecBench E. coli OOD subsets (both sources aggregated)	0.299	Not reported	Not reported	Not reported
UniSpec retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench A. thaliana OOD subset, median SAS, PepSpecBench A. thaliana OOD subset	Not reported	0.88 (best in column)	Not reported	Not reported
UniSpec retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench C. elegans OOD subset, median SAS, PepSpecBench C. elegans OOD subset	Not reported	0.812	Not reported	Not reported
UniSpec retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench E. coli OOD subsets (both sources aggregated), median SAS, PepSpecBench E. coli OOD subsets (both sources aggregated)	Not reported	0.701	Not reported	Not reported
UniSpec retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench HeLa OOD subset, median SAS, PepSpecBench HeLa OOD subset	Not reported	0.749	Not reported	Not reported
UniSpec retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench PROSPECT-Mini test split, median PCC, PepSpecBench PROSPECT-Mini test split	Not reported	Not reported	0.794	Not reported
UniSpec retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench PROSPECT-Mini test split, median SAS, PepSpecBench PROSPECT-Mini test split	Not reported	0.807	Not reported	Not reported
UniSpec retrained on PROSPECT (PepSpecBench)Evaluation	PepSpecBench Yeast OOD subset, median SAS, PepSpecBench Yeast OOD subset	Not reported	0.706	Not reported	Not reported

All 14 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: UniSpec retrained on PROSPECT (PepSpecBench)	Protocol: PepSpecBench A. thaliana OOD subset, median SA Dataset: PepSpecBench A. thaliana OOD subset	0.12 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 checked Methods, coverage and source UniSpec (trained on PROSPECT) on A. thaliana OOD subset, SA lit-otheromics-20261011-pepspecbench-protocol-a-thaliana-sa Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 4, block 'PROSPECT Trained', row 'UniSpec', column 'A. thaliana' (first value of SA / SAS)
Configuration: UniSpec retrained on PROSPECT (PepSpecBench)	Protocol: PepSpecBench A. thaliana OOD subset, median SAS Dataset: PepSpecBench A. thaliana OOD subset	0.88 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 A. thaliana OOD subset, SAS lit-otheromics-20261011-pepspecbench-protocol-a-thaliana-sas Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 4, block 'PROSPECT Trained', row 'UniSpec', column 'A. thaliana' (second value of SA / SAS)
Configuration: UniSpec retrained on PROSPECT (PepSpecBench)	Protocol: PepSpecBench C. elegans OOD subset, median SA Dataset: PepSpecBench C. elegans OOD subset	0.188 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 checked Methods, coverage and source UniSpec (trained on PROSPECT) on C. elegans OOD subset, SA lit-otheromics-20261011-pepspecbench-protocol-c-elegans-sa Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 4, block 'PROSPECT Trained', row 'UniSpec', column 'C. elegans' (first value of SA / SAS)
Configuration: UniSpec retrained on PROSPECT (PepSpecBench)	Protocol: PepSpecBench C. elegans OOD subset, median SAS Dataset: PepSpecBench C. elegans OOD subset	0.812 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 C. elegans OOD subset, SAS lit-otheromics-20261011-pepspecbench-protocol-c-elegans-sas Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 4, block 'PROSPECT Trained', row 'UniSpec', column 'C. elegans' (second value of SA / SAS)
Configuration: UniSpec retrained on PROSPECT (PepSpecBench)	Protocol: PepSpecBench E. coli OOD subsets (both sources aggregated), median SA Dataset: PepSpecBench E. coli OOD subsets (both sources aggregated)	0.299 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 checked Methods, coverage and source UniSpec (trained on PROSPECT) on E. coli OOD subsets (both sources aggregated), SA lit-otheromics-20261011-pepspecbench-protocol-e-coli-sa Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 4, block 'PROSPECT Trained', row 'UniSpec', column 'E. coli' (first value of SA / SAS)
Configuration: UniSpec retrained on PROSPECT (PepSpecBench)	Protocol: PepSpecBench E. coli OOD subsets (both sources aggregated), median SAS Dataset: PepSpecBench E. coli OOD subsets (both sources aggregated)	0.701 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 E. coli OOD subsets (both sources aggregated), SAS lit-otheromics-20261011-pepspecbench-protocol-e-coli-sas Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 4, block 'PROSPECT Trained', row 'UniSpec', column 'E. coli' (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 checked Methods, coverage and source UniSpec (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 checked Methods, coverage and source UniSpec (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)
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'
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 checked Methods, coverage and source UniSpec (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 checked Methods, coverage and source UniSpec (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 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'
Configuration: UniSpec retrained on PROSPECT (PepSpecBench)	Protocol: PepSpecBench Yeast OOD subset, median SA Dataset: PepSpecBench Yeast OOD subset	0.294 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 checked Methods, coverage and source UniSpec (trained on PROSPECT) on Yeast OOD subset, SA lit-otheromics-20261011-pepspecbench-protocol-yeast-sa Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 4, block 'PROSPECT Trained', row 'UniSpec', column 'Yeast' (first value of SA / SAS)
Configuration: UniSpec retrained on PROSPECT (PepSpecBench)	Protocol: PepSpecBench Yeast OOD subset, median SAS Dataset: PepSpecBench Yeast OOD subset	0.706 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 Yeast OOD subset, SAS lit-otheromics-20261011-pepspecbench-protocol-yeast-sas Aggregation: Not reported PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Table 4, block 'PROSPECT Trained', row 'UniSpec', column 'Yeast' (second value of SA / SAS)

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

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

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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-config-unispec-trained-prospect

areas: proteins-complexes
contexts: research
method types: supervised_machine_learning
reported name: UniSpec
foundation model eligible: false
parameters: Retrained on the PROSPECT-Mini backbone-disjoint training split (500k/50k/50k train/validation/test); outputs projected to the shared canonical b/y fragment space; hyperparameters in Appendix Table 12
training setting: Trained on PROSPECT
access reuse: Benchmark data at https://huggingface.co/datasets/Chris-young-2004/PepSpecBench; model code not stated
source locator: Section 3.2; Appendix E and Table 12
missing metadata: version: reason: unreported; note: No model or code version is printed

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