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UniSpec retrained on MassIVE-KB (PepSpecBench)

UniSpec retrained by the PepSpecBench authors on the MassIVE-KB 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 MassIVE-KB (PepSpecBench)Evaluation	PepSpecBench MassIVE-KB-Mini test split, median SA, PepSpecBench MassIVE-KB-Mini test split	0.337 (best in column)	Not reported	Not reported	0.337
UniSpec retrained on MassIVE-KB (PepSpecBench)Evaluation	PepSpecBench HeLa OOD subset, median SA, PepSpecBench HeLa OOD subset	0.38	Not reported	Not reported	Not reported
UniSpec retrained on MassIVE-KB (PepSpecBench)Evaluation	PepSpecBench C. elegans OOD subset, median SA, PepSpecBench C. elegans OOD subset	0.382	Not reported	Not reported	Not reported
UniSpec retrained on MassIVE-KB (PepSpecBench)Evaluation	PepSpecBench A. thaliana OOD subset, median SA, PepSpecBench A. thaliana OOD subset	0.384	Not reported	Not reported	Not reported
UniSpec retrained on MassIVE-KB (PepSpecBench)Evaluation	PepSpecBench E. coli OOD subsets (both sources aggregated), median SA, PepSpecBench E. coli OOD subsets (both sources aggregated)	0.388	Not reported	Not reported	Not reported
UniSpec retrained on MassIVE-KB (PepSpecBench)Evaluation	PepSpecBench Yeast OOD subset, median SA, PepSpecBench Yeast OOD subset	0.393	Not reported	Not reported	Not reported
UniSpec retrained on MassIVE-KB (PepSpecBench)Evaluation	PepSpecBench A. thaliana OOD subset, median SAS, PepSpecBench A. thaliana OOD subset	Not reported	0.616	Not reported	Not reported
UniSpec retrained on MassIVE-KB (PepSpecBench)Evaluation	PepSpecBench C. elegans OOD subset, median SAS, PepSpecBench C. elegans OOD subset	Not reported	0.618	Not reported	Not reported
UniSpec retrained on MassIVE-KB (PepSpecBench)Evaluation	PepSpecBench E. coli OOD subsets (both sources aggregated), median SAS, PepSpecBench E. coli OOD subsets (both sources aggregated)	Not reported	0.612	Not reported	Not reported
UniSpec retrained on MassIVE-KB (PepSpecBench)Evaluation	PepSpecBench HeLa OOD subset, median SAS, PepSpecBench HeLa OOD subset	Not reported	0.62	Not reported	Not reported
UniSpec retrained on MassIVE-KB (PepSpecBench)Evaluation	PepSpecBench MassIVE-KB-Mini test split, median PCC, PepSpecBench MassIVE-KB-Mini test split	Not reported	Not reported	0.048	Not reported
UniSpec retrained on MassIVE-KB (PepSpecBench)Evaluation	PepSpecBench MassIVE-KB-Mini test split, median SAS, PepSpecBench MassIVE-KB-Mini test split	Not reported	0.663 (best in column)	Not reported	Not reported
UniSpec retrained on MassIVE-KB (PepSpecBench)Evaluation	PepSpecBench Yeast OOD subset, median SAS, PepSpecBench Yeast OOD subset	Not reported	0.607	Not reported	Not reported

All 14 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: UniSpec retrained on MassIVE-KB (PepSpecBench)	Protocol: PepSpecBench A. thaliana OOD subset, median SA Dataset: PepSpecBench A. thaliana OOD subset	0.384 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 MassIVE-KB) 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 'MassIVE-KB Trained', row 'UniSpec', column 'A. thaliana' (first value of SA / SAS)
Configuration: UniSpec retrained on MassIVE-KB (PepSpecBench)	Protocol: PepSpecBench A. thaliana OOD subset, median SAS Dataset: PepSpecBench A. thaliana OOD subset	0.616 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 MassIVE-KB) 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 'MassIVE-KB Trained', row 'UniSpec', column 'A. thaliana' (second value of SA / SAS)
Configuration: UniSpec retrained on MassIVE-KB (PepSpecBench)	Protocol: PepSpecBench C. elegans OOD subset, median SA Dataset: PepSpecBench C. elegans OOD subset	0.382 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 MassIVE-KB) 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 'MassIVE-KB Trained', row 'UniSpec', column 'C. elegans' (first value of SA / SAS)
Configuration: UniSpec retrained on MassIVE-KB (PepSpecBench)	Protocol: PepSpecBench C. elegans OOD subset, median SAS Dataset: PepSpecBench C. elegans OOD subset	0.618 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 MassIVE-KB) 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 'MassIVE-KB Trained', row 'UniSpec', column 'C. elegans' (second value of SA / SAS)
Configuration: UniSpec retrained on MassIVE-KB (PepSpecBench)	Protocol: PepSpecBench E. coli OOD subsets (both sources aggregated), median SA Dataset: PepSpecBench E. coli OOD subsets (both sources aggregated)	0.388 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 MassIVE-KB) 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 'MassIVE-KB Trained', row 'UniSpec', column 'E. coli' (first value of SA / SAS)
Configuration: UniSpec retrained on MassIVE-KB (PepSpecBench)	Protocol: PepSpecBench E. coli OOD subsets (both sources aggregated), median SAS Dataset: PepSpecBench E. coli OOD subsets (both sources aggregated)	0.612 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 MassIVE-KB) 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 'MassIVE-KB Trained', row 'UniSpec', column 'E. coli' (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 checked Methods, coverage and source UniSpec (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 checked Methods, coverage and source UniSpec (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 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 checked Methods, coverage and source UniSpec (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 checked Methods, coverage and source UniSpec (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 checked Methods, coverage and source UniSpec (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 checked Methods, coverage and source UniSpec (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'
Configuration: UniSpec retrained on MassIVE-KB (PepSpecBench)	Protocol: PepSpecBench Yeast OOD subset, median SA Dataset: PepSpecBench Yeast OOD subset	0.393 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 MassIVE-KB) 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 'MassIVE-KB Trained', row 'UniSpec', column 'Yeast' (first value of SA / SAS)
Configuration: UniSpec retrained on MassIVE-KB (PepSpecBench)	Protocol: PepSpecBench Yeast OOD subset, median SAS Dataset: PepSpecBench Yeast OOD subset	0.607 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 MassIVE-KB) 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 'MassIVE-KB 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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Claims, original sources and review scope · 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-massive-kb

areas: proteins-complexes
contexts: research
method types: supervised_machine_learning
reported name: UniSpec
foundation model eligible: false
parameters: Retrained on the MassIVE-KB-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 MassIVE-KB
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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