rewirebio.iobenchmarks
Dataset

PepSpecBench MassIVE-KB-Mini test split

MassIVE-KB v1 human subset, 50k test spectra, backbone-disjoint from training; natural PTM distribution.

Evaluation results

18 evaluations · 24 results. Different protocols are not a single leaderboard.

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

Uncertainty: 95% CI 0.4752 to 0.4762. 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

FastSpel (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 'FastSpel', column 'Med. SA'
Configuration: FastSpel retrained on MassIVE-KB (PepSpecBench)Protocol: PepSpecBench MassIVE-KB-Mini test split, median SA
Dataset: PepSpecBench MassIVE-KB-Mini test split
0.476 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

FastSpel (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 'FastSpel', column group 'MassIVE-KB', column 'SA'
Configuration: FastSpel retrained on MassIVE-KB (PepSpecBench)Protocol: PepSpecBench MassIVE-KB-Mini test split, median SAS
Dataset: PepSpecBench MassIVE-KB-Mini test split
0.524 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

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

Uncertainty: 95% CI 0.1666 to 0.1680. 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

PredFull (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 'PredFull', column 'Med. SA'
Configuration: PredFull retrained on MassIVE-KB (PepSpecBench)Protocol: PepSpecBench MassIVE-KB-Mini test split, median SA
Dataset: PepSpecBench MassIVE-KB-Mini test split
0.167 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

PredFull (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 'PredFull', column group 'MassIVE-KB', column 'SA'
Configuration: PredFull retrained on MassIVE-KB (PepSpecBench)Protocol: PepSpecBench MassIVE-KB-Mini test split, median SAS
Dataset: PepSpecBench MassIVE-KB-Mini test split
0.833 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

PredFull (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 'PredFull', column group 'MassIVE-KB', column 'SAS'
Configuration: Prosit retrained on MassIVE-KB (PepSpecBench)Protocol: PepSpecBench MassIVE-KB-Mini test split, median PCC
Dataset: PepSpecBench MassIVE-KB-Mini test split
0.949 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 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 'Prosit', column group 'MassIVE-KB', column 'PCC'
Configuration: Prosit retrained on MassIVE-KB (PepSpecBench)Protocol: PepSpecBench MassIVE-KB-Mini test split, median SA
Dataset: PepSpecBench MassIVE-KB-Mini test split
0.0995 Spectral angle (median over spectra, shared canonical fragment space; four-decimal value with 95% bootstrap CI (Table 14))
unitless · lower

Uncertainty: 95% CI 0.0984 to 0.1006. 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

Prosit (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 'Prosit', column 'Med. SA'
Configuration: Prosit retrained on MassIVE-KB (PepSpecBench)Protocol: PepSpecBench MassIVE-KB-Mini test split, median SA
Dataset: PepSpecBench MassIVE-KB-Mini test split
0.1 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

Prosit (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 'Prosit', column group 'MassIVE-KB', column 'SA'
Configuration: Prosit retrained on MassIVE-KB (PepSpecBench)Protocol: PepSpecBench MassIVE-KB-Mini test split, median SAS
Dataset: PepSpecBench MassIVE-KB-Mini test split
0.901 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

Prosit (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 'Prosit', column group 'MassIVE-KB', column 'SAS'
Configuration: Prosit Transformer retrained on MassIVE-KB (PepSpecBench)Protocol: PepSpecBench MassIVE-KB-Mini test split, median PCC
Dataset: PepSpecBench MassIVE-KB-Mini test split
0.951 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 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 'Prosit Trans.', column group 'MassIVE-KB', column 'PCC'
Configuration: Prosit Transformer retrained on MassIVE-KB (PepSpecBench)Protocol: PepSpecBench MassIVE-KB-Mini test split, median SA
Dataset: PepSpecBench MassIVE-KB-Mini test split
0.0977 Spectral angle (median over spectra, shared canonical fragment space; four-decimal value with 95% bootstrap CI (Table 14))
unitless · lower

Uncertainty: 95% CI 0.0969 to 0.0986. 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

Prosit Transformer (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 'Prosit Trans.', column 'Med. SA'
Configuration: Prosit Transformer retrained on MassIVE-KB (PepSpecBench)Protocol: PepSpecBench MassIVE-KB-Mini test split, median SA
Dataset: PepSpecBench MassIVE-KB-Mini test split
0.098 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

Prosit Transformer (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 'Prosit Trans.', column group 'MassIVE-KB', column 'SA'
Configuration: Prosit Transformer retrained on MassIVE-KB (PepSpecBench)Protocol: PepSpecBench MassIVE-KB-Mini test split, median SAS
Dataset: PepSpecBench MassIVE-KB-Mini test split
0.902 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

Prosit Transformer (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 'Prosit Trans.', column group 'MassIVE-KB', column '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'

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

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Readiness checks, gaps and artifacts

Release 2026-10-23-5347695500ed · Evidence verified: Not verified

Evidence incomplete

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Exact outcomes, predictions, identifiers and evaluator are connected.

Missing or unresolved evidence

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  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

Missing or unresolved evidence

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  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified
  • Sample annotations are recorded: not yet verified
  • Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
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Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Independent validation data exist: not yet verified
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Verified: Not verified

Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.

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Dataset and evaluation context

A dataset supplies biological observations. The evaluation protocol defines how those observations are split, used and scored.

Evidence

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Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

5 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-23-5347695500ed
Property and statementOriginal source and locationReview and provenance
Source location
Table 1; Appendix C.1 and C.6
Context-only references
PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction

Original source ↗

Table 1; Appendix C.1 and C.6

Version: arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering
Retrieved: 2026-10-11T21:27:08Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.source_locator

Source artifact SHA-256: af7ed6d4470f0d4f60fccbe55103e72b19c258e53f9dd26c0c0e152a2ef18d81

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Split
Test
Context-only references
PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction

Original source ↗

Table 1; Appendix C.1 and C.6

Version: arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering
Retrieved: 2026-10-11T21:27:08Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.split

Source artifact SHA-256: af7ed6d4470f0d4f60fccbe55103e72b19c258e53f9dd26c0c0e152a2ef18d81

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Version
PepSpecBench v1
Context-only references
PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction

Original source ↗

Table 1; Appendix C.1 and C.6

Version: arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering
Retrieved: 2026-10-11T21:27:08Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.version

Source artifact SHA-256: af7ed6d4470f0d4f60fccbe55103e72b19c258e53f9dd26c0c0e152a2ef18d81

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Description
MassIVE-KB v1 human subset, 50k test spectra, backbone-disjoint from training; natural PTM distribution.
Context-only references
PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction

Original source ↗

Table 1; Appendix C.1 and C.6

Version: arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering
Retrieved: 2026-10-11T21:27:08Z

not individually reviewed

No individual claim review recorded

Audit details

Field: description

Source artifact SHA-256: af7ed6d4470f0d4f60fccbe55103e72b19c258e53f9dd26c0c0e152a2ef18d81

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Name
PepSpecBench MassIVE-KB-Mini test split
Context-only references
PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction

Original source ↗

Table 1; Appendix C.1 and C.6

Version: arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering
Retrieved: 2026-10-11T21:27:08Z

not individually reviewed

No individual claim review recorded

Audit details

Field: name

Source artifact SHA-256: af7ed6d4470f0d4f60fccbe55103e72b19c258e53f9dd26c0c0e152a2ef18d81

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Sources and history

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

1 source record and release historyDownload this release (gzip)
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Stable ID: lit-otheromics-20261011-pepspecbench-data-massive-kb

areas
proteins-complexes
contexts
research
version
PepSpecBench v1
split
Test
source locator
Table 1; Appendix C.1 and C.6
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