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Protocol

PepSpecBench MassIVE-KB-Mini test split, median SAS

In-domain test on the backbone-disjoint split; median SAS over spectra in the shared canonical fragment space.

6 evaluations · 6 results

Overview

An explanatory profile has not yet been reviewed for this record.

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

6 recorded evaluations, 6 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

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All evaluations

6 evaluations · 6 results. Different protocols are not a single leaderboard.

Protocol: PepSpecBench MassIVE-KB-Mini test split, median SAS · Dataset: PepSpecBench MassIVE-KB-Mini test split

Sorted by Spectral angle similarity (median over spectra, shared canonical fragment space) (higher 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 configurationSpectral angle similarity (median over spectra, shared canonical fragment space)
Prosit Transformer retrained on MassIVE-KB (PepSpecBench)Evaluation0.902 (best in column)
Prosit retrained on MassIVE-KB (PepSpecBench)Evaluation0.901
AlphaPeptDeep retrained on MassIVE-KB (PepSpecBench)Evaluation0.871
PredFull retrained on MassIVE-KB (PepSpecBench)Evaluation0.833
UniSpec retrained on MassIVE-KB (PepSpecBench)Evaluation0.663
FastSpel retrained on MassIVE-KB (PepSpecBench)Evaluation0.524
All 6 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 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 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 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 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 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 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.

Methods and evaluation design

Procedure, tasks and evaluated configurations

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

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External evaluations
6

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Null control

Proposed control: requires review

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Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

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Conventional reference

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Select an upstream conventional reference after reviewing the full protocol

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Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

Coverage is derived from release 2026-10-23-5347695500ed. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

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Evidence

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Evidence table

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Claims, original sources and review scope · Release 2026-10-23-5347695500ed
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Sources and history

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

1 source record and release historyDownload this release (gzip)
Technical metadata and extraction receipts

Stable ID: lit-otheromics-20261011-pepspecbench-protocol-massive-kb-sas

areas
proteins-complexes
contexts
research
protocol
Predict fragment intensities for each spectrum, project to the shared canonical b/y space, mask invalid positions, compute SAS per spectrum and take the median.
version
PepSpecBench v1
metric
spectral-angle-similarity
metric direction
higher
unit
unitless
metric qualifier
median over spectra, shared canonical fragment space
source locator
Section 3.3 (metrics and evaluation protocol); Table 2
limitations
Preprint.; Medians, not means.
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