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AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)

AlphaPeptDeep retrained by the PepSpecBench authors on the MassIVE-KB backbone-disjoint training split (500k spectra).

13 evaluations · 14 results

Overview

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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

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 configurationProtocol and datasetSpectral 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))
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)EvaluationPepSpecBench MassIVE-KB-Mini test split, median SA, PepSpecBench MassIVE-KB-Mini test split0.129 (best in column)Not reportedNot reported0.129
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)EvaluationPepSpecBench HeLa OOD subset, median SA, PepSpecBench HeLa OOD subset0.468Not reportedNot reportedNot reported
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)EvaluationPepSpecBench C. elegans OOD subset, median SA, PepSpecBench C. elegans OOD subset0.47Not reportedNot reportedNot reported
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)EvaluationPepSpecBench E. coli OOD subsets (both sources aggregated), median SA, PepSpecBench E. coli OOD subsets (both sources aggregated)0.473Not reportedNot reportedNot reported
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)EvaluationPepSpecBench Yeast OOD subset, median SA, PepSpecBench Yeast OOD subset0.473Not reportedNot reportedNot reported
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)EvaluationPepSpecBench A. thaliana OOD subset, median SA, PepSpecBench A. thaliana OOD subset0.482Not reportedNot reportedNot reported
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)EvaluationPepSpecBench A. thaliana OOD subset, median SAS, PepSpecBench A. thaliana OOD subsetNot reported0.518Not reportedNot reported
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)EvaluationPepSpecBench C. elegans OOD subset, median SAS, PepSpecBench C. elegans OOD subsetNot reported0.53Not reportedNot reported
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)EvaluationPepSpecBench E. coli OOD subsets (both sources aggregated), median SAS, PepSpecBench E. coli OOD subsets (both sources aggregated)Not reported0.527Not reportedNot reported
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)EvaluationPepSpecBench HeLa OOD subset, median SAS, PepSpecBench HeLa OOD subsetNot reported0.532Not reportedNot reported
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)EvaluationPepSpecBench MassIVE-KB-Mini test split, median PCC, PepSpecBench MassIVE-KB-Mini test splitNot reportedNot reported0.915Not reported
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)EvaluationPepSpecBench MassIVE-KB-Mini test split, median SAS, PepSpecBench MassIVE-KB-Mini test splitNot reported0.871 (best in column)Not reportedNot reported
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)EvaluationPepSpecBench Yeast OOD subset, median SAS, PepSpecBench Yeast OOD subsetNot reported0.527Not reportedNot reported
All 14 result rows with coverage, uncertainty and sources
Filter evaluations

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)Protocol: PepSpecBench A. thaliana OOD subset, median SA
Dataset: PepSpecBench A. thaliana OOD subset		0.482 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

AlphaPeptDeep (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 'AlphaPep.', column 'A. thaliana' (first value of SA / SAS)
Configuration: AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)Protocol: PepSpecBench A. thaliana OOD subset, median SAS
Dataset: PepSpecBench A. thaliana OOD subset		0.518 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 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 'AlphaPep.', column 'A. thaliana' (second value of SA / SAS)
Configuration: AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)Protocol: PepSpecBench C. elegans OOD subset, median SA
Dataset: PepSpecBench C. elegans OOD subset		0.47 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

AlphaPeptDeep (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 'AlphaPep.', column 'C. elegans' (first value of SA / SAS)
Configuration: AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)Protocol: PepSpecBench C. elegans OOD subset, median SAS
Dataset: PepSpecBench C. elegans OOD subset		0.53 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 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 'AlphaPep.', column 'C. elegans' (second value of SA / SAS)
Configuration: AlphaPeptDeep 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)		0.473 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

AlphaPeptDeep (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 'AlphaPep.', column 'E. coli' (first value of SA / SAS)
Configuration: AlphaPeptDeep 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)		0.527 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 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 'AlphaPep.', column 'E. coli' (second value of SA / SAS)
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 checked
Methods, coverage and source

AlphaPeptDeep (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 checked
Methods, coverage and source

AlphaPeptDeep (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 MassIVE-KB (PepSpecBench)Protocol: PepSpecBench MassIVE-KB-Mini test split, median PCC
Dataset: PepSpecBench MassIVE-KB-Mini test split		0.915 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 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 'AlphaPeptDeep', column group 'MassIVE-KB', column 'PCC'
Configuration: AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)Protocol: PepSpecBench MassIVE-KB-Mini test split, median SA
Dataset: PepSpecBench MassIVE-KB-Mini test split		0.129 Spectral angle (median over spectra, shared canonical fragment space; four-decimal value with 95% bootstrap CI (Table 14))
unitless · lower

Uncertainty: 95% CI 0.1277 to 0.1300. 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

AlphaPeptDeep (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 'AlphaPeptDeep', column 'Med. SA'
Configuration: AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)Protocol: PepSpecBench MassIVE-KB-Mini test split, median SA
Dataset: PepSpecBench MassIVE-KB-Mini test split		0.129 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

AlphaPeptDeep (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 'AlphaPeptDeep', column group 'MassIVE-KB', column 'SA'
Configuration: AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)Protocol: PepSpecBench MassIVE-KB-Mini test split, median SAS
Dataset: PepSpecBench MassIVE-KB-Mini test split		0.871 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 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 'AlphaPeptDeep', column group 'MassIVE-KB', column 'SAS'
Configuration: AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)Protocol: PepSpecBench Yeast OOD subset, median SA
Dataset: PepSpecBench Yeast OOD subset		0.473 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

AlphaPeptDeep (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 'AlphaPep.', column 'Yeast' (first value of SA / SAS)
Configuration: AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)Protocol: PepSpecBench Yeast OOD subset, median SAS
Dataset: PepSpecBench Yeast OOD subset		0.527 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 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 'AlphaPep.', 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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Technical metadata and extraction receipts

Stable ID: lit-otheromics-20261011-pepspecbench-config-alphapeptdeep-trained-massive-kb

areas
proteins-complexes
contexts
research
method types
supervised_machine_learning
reported name
AlphaPeptDeep
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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