Source

PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction

arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering · Preprint

DOI: 10.48550/arXiv.2605.01945 Original source

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Records in this release that cite this source. A record can cite several sources.

6 models
12 configurations
1 benchmark
16 protocols
7 datasets
156 evaluations
168 results

Results

Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.

Model or configuration	Metric	Value	Dataset	Evaluation
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space)	0.482 unitless	PepSpecBench A. thaliana OOD subset	AlphaPeptDeep (trained on MassIVE-KB) on A. thaliana OOD subset, SA
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)	Spectral angle similarity (median over spectra, shared canonical fragment space)	0.518 unitless	PepSpecBench A. thaliana OOD subset	AlphaPeptDeep (trained on MassIVE-KB) on A. thaliana OOD subset, SAS
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space)	0.470 unitless	PepSpecBench C. elegans OOD subset	AlphaPeptDeep (trained on MassIVE-KB) on C. elegans OOD subset, SA
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)	Spectral angle similarity (median over spectra, shared canonical fragment space)	0.530 unitless	PepSpecBench C. elegans OOD subset	AlphaPeptDeep (trained on MassIVE-KB) on C. elegans OOD subset, SAS
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space)	0.473 unitless	PepSpecBench E. coli OOD subsets (both sources aggregated)	AlphaPeptDeep (trained on MassIVE-KB) on E. coli OOD subsets (both sources aggregated), SA
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)	Spectral angle similarity (median over spectra, shared canonical fragment space)	0.527 unitless	PepSpecBench E. coli OOD subsets (both sources aggregated)	AlphaPeptDeep (trained on MassIVE-KB) on E. coli OOD subsets (both sources aggregated), SAS
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space)	0.468 unitless	PepSpecBench HeLa OOD subset	AlphaPeptDeep (trained on MassIVE-KB) on HeLa OOD subset, SA
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)	Spectral angle similarity (median over spectra, shared canonical fragment space)	0.532 unitless	PepSpecBench HeLa OOD subset	AlphaPeptDeep (trained on MassIVE-KB) on HeLa OOD subset, SAS
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)	Pearson (median over spectra, shared canonical fragment space)	0.915 unitless	PepSpecBench MassIVE-KB-Mini test split	AlphaPeptDeep (trained on MassIVE-KB) on MassIVE-KB-Mini test split, PCC
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space)	0.129 unitless	PepSpecBench MassIVE-KB-Mini test split	AlphaPeptDeep (trained on MassIVE-KB) on MassIVE-KB-Mini test split, SA
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space; four-decimal value with 95% bootstrap CI (Table 14))	0.1288 unitless	PepSpecBench MassIVE-KB-Mini test split	AlphaPeptDeep (trained on MassIVE-KB) on MassIVE-KB-Mini test split, SA
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)	Spectral angle similarity (median over spectra, shared canonical fragment space)	0.871 unitless	PepSpecBench MassIVE-KB-Mini test split	AlphaPeptDeep (trained on MassIVE-KB) on MassIVE-KB-Mini test split, SAS
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space)	0.473 unitless	PepSpecBench Yeast OOD subset	AlphaPeptDeep (trained on MassIVE-KB) on Yeast OOD subset, SA
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)	Spectral angle similarity (median over spectra, shared canonical fragment space)	0.527 unitless	PepSpecBench Yeast OOD subset	AlphaPeptDeep (trained on MassIVE-KB) on Yeast OOD subset, SAS
AlphaPeptDeep retrained on PROSPECT (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space)	0.157 unitless	PepSpecBench A. thaliana OOD subset	AlphaPeptDeep (trained on PROSPECT) on A. thaliana OOD subset, SA
AlphaPeptDeep retrained on PROSPECT (PepSpecBench)	Spectral angle similarity (median over spectra, shared canonical fragment space)	0.843 unitless	PepSpecBench A. thaliana OOD subset	AlphaPeptDeep (trained on PROSPECT) on A. thaliana OOD subset, SAS
AlphaPeptDeep retrained on PROSPECT (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space)	0.246 unitless	PepSpecBench C. elegans OOD subset	AlphaPeptDeep (trained on PROSPECT) on C. elegans OOD subset, SA
AlphaPeptDeep retrained on PROSPECT (PepSpecBench)	Spectral angle similarity (median over spectra, shared canonical fragment space)	0.754 unitless	PepSpecBench C. elegans OOD subset	AlphaPeptDeep (trained on PROSPECT) on C. elegans OOD subset, SAS
AlphaPeptDeep retrained on PROSPECT (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space)	0.312 unitless	PepSpecBench E. coli OOD subsets (both sources aggregated)	AlphaPeptDeep (trained on PROSPECT) on E. coli OOD subsets (both sources aggregated), SA
AlphaPeptDeep retrained on PROSPECT (PepSpecBench)	Spectral angle similarity (median over spectra, shared canonical fragment space)	0.688 unitless	PepSpecBench E. coli OOD subsets (both sources aggregated)	AlphaPeptDeep (trained on PROSPECT) on E. coli OOD subsets (both sources aggregated), SAS
AlphaPeptDeep retrained on PROSPECT (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space)	0.274 unitless	PepSpecBench HeLa OOD subset	AlphaPeptDeep (trained on PROSPECT) on HeLa OOD subset, SA
AlphaPeptDeep retrained on PROSPECT (PepSpecBench)	Spectral angle similarity (median over spectra, shared canonical fragment space)	0.726 unitless	PepSpecBench HeLa OOD subset	AlphaPeptDeep (trained on PROSPECT) on HeLa OOD subset, SAS
AlphaPeptDeep retrained on PROSPECT (PepSpecBench)	Pearson (median over spectra, shared canonical fragment space)	0.593 unitless	PepSpecBench PROSPECT-Mini test split	AlphaPeptDeep (trained on PROSPECT) on PROSPECT-Mini test split, PCC
AlphaPeptDeep retrained on PROSPECT (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space)	0.278 unitless	PepSpecBench PROSPECT-Mini test split	AlphaPeptDeep (trained on PROSPECT) on PROSPECT-Mini test split, SA
AlphaPeptDeep retrained on PROSPECT (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space; four-decimal value with 95% bootstrap CI (Table 14))	0.2779 unitless	PepSpecBench PROSPECT-Mini test split	AlphaPeptDeep (trained on PROSPECT) on PROSPECT-Mini test split, SA
AlphaPeptDeep retrained on PROSPECT (PepSpecBench)	Spectral angle similarity (median over spectra, shared canonical fragment space)	0.722 unitless	PepSpecBench PROSPECT-Mini test split	AlphaPeptDeep (trained on PROSPECT) on PROSPECT-Mini test split, SAS
AlphaPeptDeep retrained on PROSPECT (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space)	0.319 unitless	PepSpecBench Yeast OOD subset	AlphaPeptDeep (trained on PROSPECT) on Yeast OOD subset, SA
AlphaPeptDeep retrained on PROSPECT (PepSpecBench)	Spectral angle similarity (median over spectra, shared canonical fragment space)	0.681 unitless	PepSpecBench Yeast OOD subset	AlphaPeptDeep (trained on PROSPECT) on Yeast OOD subset, SAS
FastSpel retrained on MassIVE-KB (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space)	0.469 unitless	PepSpecBench A. thaliana OOD subset	FastSpel (trained on MassIVE-KB) on A. thaliana OOD subset, SA
FastSpel retrained on MassIVE-KB (PepSpecBench)	Spectral angle similarity (median over spectra, shared canonical fragment space)	0.531 unitless	PepSpecBench A. thaliana OOD subset	FastSpel (trained on MassIVE-KB) on A. thaliana OOD subset, SAS
FastSpel retrained on MassIVE-KB (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space)	0.476 unitless	PepSpecBench C. elegans OOD subset	FastSpel (trained on MassIVE-KB) on C. elegans OOD subset, SA
FastSpel retrained on MassIVE-KB (PepSpecBench)	Spectral angle similarity (median over spectra, shared canonical fragment space)	0.524 unitless	PepSpecBench C. elegans OOD subset	FastSpel (trained on MassIVE-KB) on C. elegans OOD subset, SAS
FastSpel retrained on MassIVE-KB (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space)	0.465 unitless	PepSpecBench E. coli OOD subsets (both sources aggregated)	FastSpel (trained on MassIVE-KB) on E. coli OOD subsets (both sources aggregated), SA
FastSpel retrained on MassIVE-KB (PepSpecBench)	Spectral angle similarity (median over spectra, shared canonical fragment space)	0.535 unitless	PepSpecBench E. coli OOD subsets (both sources aggregated)	FastSpel (trained on MassIVE-KB) on E. coli OOD subsets (both sources aggregated), SAS
FastSpel retrained on MassIVE-KB (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space)	0.461 unitless	PepSpecBench HeLa OOD subset	FastSpel (trained on MassIVE-KB) on HeLa OOD subset, SA
FastSpel retrained on MassIVE-KB (PepSpecBench)	Spectral angle similarity (median over spectra, shared canonical fragment space)	0.539 unitless	PepSpecBench HeLa OOD subset	FastSpel (trained on MassIVE-KB) on HeLa OOD subset, SAS
FastSpel retrained on MassIVE-KB (PepSpecBench)	Pearson (median over spectra, shared canonical fragment space)	0.010 unitless	PepSpecBench MassIVE-KB-Mini test split	FastSpel (trained on MassIVE-KB) on MassIVE-KB-Mini test split, PCC
FastSpel retrained on MassIVE-KB (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space)	0.476 unitless	PepSpecBench MassIVE-KB-Mini test split	FastSpel (trained on MassIVE-KB) on MassIVE-KB-Mini test split, SA
FastSpel retrained on MassIVE-KB (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space; four-decimal value with 95% bootstrap CI (Table 14))	0.4757 unitless	PepSpecBench MassIVE-KB-Mini test split	FastSpel (trained on MassIVE-KB) on MassIVE-KB-Mini test split, SA
FastSpel retrained on MassIVE-KB (PepSpecBench)	Spectral angle similarity (median over spectra, shared canonical fragment space)	0.524 unitless	PepSpecBench MassIVE-KB-Mini test split	FastSpel (trained on MassIVE-KB) on MassIVE-KB-Mini test split, SAS
FastSpel retrained on MassIVE-KB (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space)	0.461 unitless	PepSpecBench Yeast OOD subset	FastSpel (trained on MassIVE-KB) on Yeast OOD subset, SA
FastSpel retrained on MassIVE-KB (PepSpecBench)	Spectral angle similarity (median over spectra, shared canonical fragment space)	0.539 unitless	PepSpecBench Yeast OOD subset	FastSpel (trained on MassIVE-KB) on Yeast OOD subset, SAS
FastSpel retrained on PROSPECT (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space)	0.344 unitless	PepSpecBench A. thaliana OOD subset	FastSpel (trained on PROSPECT) on A. thaliana OOD subset, SA
FastSpel retrained on PROSPECT (PepSpecBench)	Spectral angle similarity (median over spectra, shared canonical fragment space)	0.656 unitless	PepSpecBench A. thaliana OOD subset	FastSpel (trained on PROSPECT) on A. thaliana OOD subset, SAS
FastSpel retrained on PROSPECT (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space)	0.392 unitless	PepSpecBench C. elegans OOD subset	FastSpel (trained on PROSPECT) on C. elegans OOD subset, SA
FastSpel retrained on PROSPECT (PepSpecBench)	Spectral angle similarity (median over spectra, shared canonical fragment space)	0.609 unitless	PepSpecBench C. elegans OOD subset	FastSpel (trained on PROSPECT) on C. elegans OOD subset, SAS
FastSpel retrained on PROSPECT (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space)	0.369 unitless	PepSpecBench E. coli OOD subsets (both sources aggregated)	FastSpel (trained on PROSPECT) on E. coli OOD subsets (both sources aggregated), SA
FastSpel retrained on PROSPECT (PepSpecBench)	Spectral angle similarity (median over spectra, shared canonical fragment space)	0.631 unitless	PepSpecBench E. coli OOD subsets (both sources aggregated)	FastSpel (trained on PROSPECT) on E. coli OOD subsets (both sources aggregated), SAS
FastSpel retrained on PROSPECT (PepSpecBench)	Spectral angle (median over spectra, shared canonical fragment space)	0.361 unitless	PepSpecBench HeLa OOD subset	FastSpel (trained on PROSPECT) on HeLa OOD subset, SA
FastSpel retrained on PROSPECT (PepSpecBench)	Spectral angle similarity (median over spectra, shared canonical fragment space)	0.639 unitless	PepSpecBench HeLa OOD subset	FastSpel (trained on PROSPECT) on HeLa OOD subset, SAS

Models, benchmarks and other records

Models (6)

Configurations (12)

Benchmarks (1)

PepSpecBench

Protocols (16)

Datasets (7)

Evaluations (156)

Evidence

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Evidence table

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19 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-23-5347695500ed
Property and statement	Original source and location	Review and provenance
Artifact SHA-256 af7ed6d4470f0d4f60fccbe55103e72b19c258e53f9dd26c0c0e152a2ef18d81 Source metadata	PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction Original source ↗ No field-specific location recorded Version: arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering Retrieved: 2026-10-11T21:27:08Z	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_sha256` Source artifact SHA-256: `af7ed6d4470f0d4f60fccbe55103e72b19c258e53f9dd26c0c0e152a2ef18d81` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Artifact url https://arxiv.org/html/2605.01945v1 Source metadata	PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction Original source ↗ No field-specific location recorded Version: arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering Retrieved: 2026-10-11T21:27:08Z	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_url` Source artifact SHA-256: `af7ed6d4470f0d4f60fccbe55103e72b19c258e53f9dd26c0c0e152a2ef18d81` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Doi 10.48550/arXiv.2605.01945 Source metadata	PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction Original source ↗ No field-specific location recorded Version: arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering Retrieved: 2026-10-11T21:27:08Z	catalogued No individual claim review recorded Audit details Field: `attributes.doi` Source artifact SHA-256: `af7ed6d4470f0d4f60fccbe55103e72b19c258e53f9dd26c0c0e152a2ef18d81` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Licence arXiv.org perpetual non-exclusive licence 1.0 (no reuse licence); not archived Source metadata	PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction Original source ↗ No field-specific location recorded Version: arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering Retrieved: 2026-10-11T21:27:08Z	catalogued No individual claim review recorded Audit details Field: `attributes.licence` Source artifact SHA-256: `af7ed6d4470f0d4f60fccbe55103e72b19c258e53f9dd26c0c0e152a2ef18d81` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Limitations 3 values The arXiv HTML is generated from the LaTeX source and may be regenerated; the hash describes one retrieval. PROSPECT PredFull in-domain SA is printed as 0.204 in Table 2 and 0.203 in Table 4 (ID column); Table 14 gives 0.2035. Table 2 SAS 0.797 implies SA 0.203. Bold marks (best per source) are not recorded. Source metadata	PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction Original source ↗ No field-specific location recorded Version: arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering Retrieved: 2026-10-11T21:27:08Z	catalogued No individual claim review recorded Audit details Field: `attributes.limitations` Source artifact SHA-256: `af7ed6d4470f0d4f60fccbe55103e72b19c258e53f9dd26c0c0e152a2ef18d81` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Media type text/html Source metadata	PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction Original source ↗ No field-specific location recorded Version: arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering Retrieved: 2026-10-11T21:27:08Z	catalogued No individual claim review recorded Audit details Field: `attributes.media_type` Source artifact SHA-256: `af7ed6d4470f0d4f60fccbe55103e72b19c258e53f9dd26c0c0e152a2ef18d81` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Publication status preprint Source metadata	PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction Original source ↗ No field-specific location recorded Version: arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering Retrieved: 2026-10-11T21:27:08Z	catalogued No individual claim review recorded Audit details Field: `attributes.publication_status` Source artifact SHA-256: `af7ed6d4470f0d4f60fccbe55103e72b19c258e53f9dd26c0c0e152a2ef18d81` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Retrieved at 2026-10-11T21:27:08Z Source metadata	PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction Original source ↗ No field-specific location recorded Version: arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering Retrieved: 2026-10-11T21:27:08Z	catalogued No individual claim review recorded Audit details Field: `attributes.retrieved_at` Source artifact SHA-256: `af7ed6d4470f0d4f60fccbe55103e72b19c258e53f9dd26c0c0e152a2ef18d81` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Url https://arxiv.org/abs/2605.01945v1 Source metadata	PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction Original source ↗ No field-specific location recorded Version: arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering Retrieved: 2026-10-11T21:27:08Z	catalogued No individual claim review recorded Audit details Field: `attributes.url` Source artifact SHA-256: `af7ed6d4470f0d4f60fccbe55103e72b19c258e53f9dd26c0c0e152a2ef18d81` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Version note The PDF of the same version (https://arxiv.org/pdf/2605.01945v1) was also retrieved, SHA-256 98da8c16b5ab6c5e8ec225f0807ff2b9143fbb0f4d34cef0f3aa79c9b738a2de; values were read from the HTML tables. Source metadata	PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction Original source ↗ No field-specific location recorded Version: arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering Retrieved: 2026-10-11T21:27:08Z	catalogued No individual claim review recorded Audit details Field: `attributes.version_note` Source artifact SHA-256: `af7ed6d4470f0d4f60fccbe55103e72b19c258e53f9dd26c0c0e152a2ef18d81` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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

Primary source retrieved and hashed for the 2026-10-11 RNA and other-omics literature pass.

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Technical metadata and extraction receipts

Stable ID: lit-otheromics-20261011-pepspecbench-source-yang2026

areas: proteins-complexes
contexts: research
url: https://arxiv.org/abs/2605.01945v1
artifact url: https://arxiv.org/html/2605.01945v1
version: arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering
version note: The PDF of the same version (https://arxiv.org/pdf/2605.01945v1) was also retrieved, SHA-256 98da8c16b5ab6c5e8ec225f0807ff2b9143fbb0f4d34cef0f3aa79c9b738a2de; values were read from the HTML tables.
retrieved at: 2026-10-11T21:27:08Z
artifact sha256: af7ed6d4470f0d4f60fccbe55103e72b19c258e53f9dd26c0c0e152a2ef18d81
doi: 10.48550/arXiv.2605.01945
publication status: preprint
licence: arXiv.org perpetual non-exclusive licence 1.0 (no reuse licence); not archived
media type: text/html
limitations: The arXiv HTML is generated from the LaTeX source and may be regenerated; the hash describes one retrieval.; PROSPECT PredFull in-domain SA is printed as 0.204 in Table 2 and 0.203 in Table 4 (ID column); Table 14 gives 0.2035. Table 2 SAS 0.797 implies SA 0.203.; Bold marks (best per source) are not recorded.

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