PepSpecBench A. thaliana OOD subset, median SAS
Zero-shot out-of-distribution transfer: models trained on one in-domain source are scored without adaptation; median SAS over spectra in the shared canonical fragment space.
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.
12 recorded evaluations, 12 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
12 evaluations · 12 results. Different protocols are not a single leaderboard.
Protocol: PepSpecBench A. thaliana OOD subset, median SAS · Dataset: PepSpecBench A. thaliana OOD subset
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.
All 12 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| 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 checkedMethods, coverage and sourceAlphaPeptDeep (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 PROSPECT (PepSpecBench) | Protocol: PepSpecBench A. thaliana OOD subset, median SAS Dataset: PepSpecBench A. thaliana OOD subset | 0.843 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 checkedMethods, coverage and sourceAlphaPeptDeep (trained on PROSPECT) 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 'PROSPECT Trained', row 'AlphaPep.', column 'A. thaliana' (second value of SA / SAS) |
| Configuration: FastSpel retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench A. thaliana OOD subset, median SAS Dataset: PepSpecBench A. thaliana OOD subset | 0.531 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 checkedMethods, coverage and sourceFastSpel (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 'FastSpel', column 'A. thaliana' (second value of SA / SAS) |
| Configuration: FastSpel retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench A. thaliana OOD subset, median SAS Dataset: PepSpecBench A. thaliana OOD subset | 0.656 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 checkedMethods, coverage and sourceFastSpel (trained on PROSPECT) 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 'PROSPECT Trained', row 'FastSpel', column 'A. thaliana' (second value of SA / SAS) |
| Configuration: PredFull retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench A. thaliana OOD subset, median SAS Dataset: PepSpecBench A. thaliana OOD subset | 0.797 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 checkedMethods, coverage and sourcePredFull (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 'PredFull', column 'A. thaliana' (second value of SA / SAS) |
| Configuration: PredFull retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench A. thaliana OOD subset, median SAS Dataset: PepSpecBench A. thaliana OOD subset | 0.837 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 checkedMethods, coverage and sourcePredFull (trained on PROSPECT) 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 'PROSPECT Trained', row 'PredFull', column 'A. thaliana' (second value of SA / SAS) |
| Configuration: Prosit retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench A. thaliana OOD subset, median SAS Dataset: PepSpecBench A. thaliana OOD subset | 0.516 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 checkedMethods, coverage and sourceProsit (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 'Prosit', column 'A. thaliana' (second value of SA / SAS) |
| Configuration: Prosit retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench A. thaliana OOD subset, median SAS Dataset: PepSpecBench A. thaliana OOD subset | 0.906 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 checkedMethods, coverage and sourceProsit (trained on PROSPECT) 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 'PROSPECT Trained', row 'Prosit', column 'A. thaliana' (second value of SA / SAS) |
| Configuration: Prosit Transformer retrained on MassIVE-KB (PepSpecBench) | Protocol: PepSpecBench A. thaliana OOD subset, median SAS Dataset: PepSpecBench A. thaliana OOD subset | 0.515 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 checkedMethods, coverage and sourceProsit Transformer (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 'Prosit Tran.', column 'A. thaliana' (second value of SA / SAS) |
| Configuration: Prosit Transformer retrained on PROSPECT (PepSpecBench) | Protocol: PepSpecBench A. thaliana OOD subset, median SAS Dataset: PepSpecBench A. thaliana OOD subset | 0.898 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 checkedMethods, coverage and sourceProsit Transformer (trained on PROSPECT) 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 'PROSPECT Trained', row 'Prosit Tran.', column 'A. thaliana' (second 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 checkedMethods, coverage and sourceUniSpec (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 PROSPECT (PepSpecBench) | Protocol: PepSpecBench A. thaliana OOD subset, median SAS Dataset: PepSpecBench A. thaliana OOD subset | 0.88 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 checkedMethods, coverage and sourceUniSpec (trained on PROSPECT) 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 'PROSPECT Trained', row 'UniSpec', column 'A. thaliana' (second value of SA / 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.
- AlphaPeptDeep (trained on MassIVE-KB) on A. thaliana OOD subset, SAS
- AlphaPeptDeep (trained on PROSPECT) on A. thaliana OOD subset, SAS
- FastSpel (trained on MassIVE-KB) on A. thaliana OOD subset, SAS
- FastSpel (trained on PROSPECT) on A. thaliana OOD subset, SAS
- PredFull (trained on MassIVE-KB) on A. thaliana OOD subset, SAS
- PredFull (trained on PROSPECT) on A. thaliana OOD subset, SAS
- Prosit (trained on MassIVE-KB) on A. thaliana OOD subset, SAS
- Prosit (trained on PROSPECT) on A. thaliana OOD subset, SAS
- Prosit Transformer (trained on MassIVE-KB) on A. thaliana OOD subset, SAS
- Prosit Transformer (trained on PROSPECT) on A. thaliana OOD subset, SAS
- UniSpec (trained on MassIVE-KB) on A. thaliana OOD subset, SAS
- UniSpec (trained on PROSPECT) on A. thaliana OOD subset, SAS
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.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
- External evaluations
- 12
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Protocol-valid seeded random ranking; no fitting on assay labels
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Established label-free reference with explicitly permitted sequence/MSA inputs
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
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
No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Evidence
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Evidence table
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Sources and history
Release 2026-10-23-5347695500ed · Record review: source checked
1 source record and release history
- PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction · Original source · arXiv:2605.01945v1 (submitted 2026-05-03), arXiv HTML rendering
Technical metadata and extraction receipts
Stable ID: lit-otheromics-20261011-pepspecbench-protocol-a-thaliana-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 4
- limitations
- Preprint.; Medians, not means.; OOD results depend on the training source; compare only within one training source.
Related records
- part of: PepSpecBench
- uses data: PepSpecBench A. thaliana OOD subset
- assessment: AlphaPeptDeep (trained on MassIVE-KB) on A. thaliana OOD subset, SAS
- assessment: AlphaPeptDeep (trained on PROSPECT) on A. thaliana OOD subset, SAS
- assessment: FastSpel (trained on MassIVE-KB) on A. thaliana OOD subset, SAS
- assessment: FastSpel (trained on PROSPECT) on A. thaliana OOD subset, SAS
- assessment: PredFull (trained on MassIVE-KB) on A. thaliana OOD subset, SAS
- assessment: PredFull (trained on PROSPECT) on A. thaliana OOD subset, SAS
- assessment: Prosit (trained on MassIVE-KB) on A. thaliana OOD subset, SAS
- assessment: Prosit (trained on PROSPECT) on A. thaliana OOD subset, SAS
- assessment: Prosit Transformer (trained on MassIVE-KB) on A. thaliana OOD subset, SAS
- assessment: Prosit Transformer (trained on PROSPECT) on A. thaliana OOD subset, SAS
- assessment: UniSpec (trained on MassIVE-KB) on A. thaliana OOD subset, SAS
- assessment: UniSpec (trained on PROSPECT) on A. thaliana OOD subset, SAS