PepSpecBench
Benchmark for peptide MS/MS fragment intensity prediction with harmonised PROSPECT and MassIVE-KB subsets, backbone-disjoint splits, a shared canonical fragment-ion evaluation space and a cross-species out-of-distribution suite.
Results are recorded on the linked protocols, tasks or configurations listed below. Their settings and evaluations are kept separate.
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.
Results on linked records
This benchmark has no results of its own in this release. 16 linked records have results. They are not assigned to the underlying benchmark: each record keeps its own settings and evaluations, and its scores are on its own page.
- PepSpecBench A. thaliana OOD subset, median SA Protocol · part of this benchmark · 12 evaluations · 12 results
- PepSpecBench A. thaliana OOD subset, median SAS Protocol · part of this benchmark · 12 evaluations · 12 results
- PepSpecBench C. elegans OOD subset, median SA Protocol · part of this benchmark · 12 evaluations · 12 results
- PepSpecBench C. elegans OOD subset, median SAS Protocol · part of this benchmark · 12 evaluations · 12 results
- PepSpecBench E. coli OOD subsets (both sources aggregated), median SA Protocol · part of this benchmark · 12 evaluations · 12 results
- PepSpecBench E. coli OOD subsets (both sources aggregated), median SAS Protocol · part of this benchmark · 12 evaluations · 12 results
- PepSpecBench HeLa OOD subset, median SA Protocol · part of this benchmark · 12 evaluations · 12 results
- PepSpecBench HeLa OOD subset, median SAS Protocol · part of this benchmark · 12 evaluations · 12 results
- PepSpecBench MassIVE-KB-Mini test split, median PCC Protocol · part of this benchmark · 6 evaluations · 6 results
- PepSpecBench MassIVE-KB-Mini test split, median SA Protocol · part of this benchmark · 6 evaluations · 12 results
- PepSpecBench MassIVE-KB-Mini test split, median SAS Protocol · part of this benchmark · 6 evaluations · 6 results
- PepSpecBench PROSPECT-Mini test split, median PCC Protocol · part of this benchmark · 6 evaluations · 6 results
- PepSpecBench PROSPECT-Mini test split, median SA Protocol · part of this benchmark · 6 evaluations · 12 results
- PepSpecBench PROSPECT-Mini test split, median SAS Protocol · part of this benchmark · 6 evaluations · 6 results
- PepSpecBench Yeast OOD subset, median SA Protocol · part of this benchmark · 12 evaluations · 12 results
- PepSpecBench Yeast OOD subset, median SAS Protocol · part of this benchmark · 12 evaluations · 12 results
Methods and evaluation design
Procedure, tasks and evaluated configurations
Additional methodological details, tasks and evaluated configurations have not yet been extracted into a structured profile for this benchmark. Consult the linked sources and evaluation records below.
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 32 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
Baseline status by linked protocol
- PepSpecBench A. thaliana OOD subset, median SA · 0/2 roles measured
- PepSpecBench A. thaliana OOD subset, median SAS · 0/2 roles measured
- PepSpecBench C. elegans OOD subset, median SA · 0/2 roles measured
- PepSpecBench C. elegans OOD subset, median SAS · 0/2 roles measured
- PepSpecBench E. coli OOD subsets (both sources aggregated), median SA · 0/2 roles measured
- PepSpecBench E. coli OOD subsets (both sources aggregated), median SAS · 0/2 roles measured
- PepSpecBench HeLa OOD subset, median SA · 0/2 roles measured
- PepSpecBench HeLa OOD subset, median SAS · 0/2 roles measured
- PepSpecBench MassIVE-KB-Mini test split, median PCC · 0/2 roles measured
- PepSpecBench MassIVE-KB-Mini test split, median SA · 0/2 roles measured
- PepSpecBench MassIVE-KB-Mini test split, median SAS · 0/2 roles measured
- PepSpecBench PROSPECT-Mini test split, median PCC · 0/2 roles measured
- PepSpecBench PROSPECT-Mini test split, median SA · 0/2 roles measured
- PepSpecBench PROSPECT-Mini test split, median SAS · 0/2 roles measured
- PepSpecBench Yeast OOD subset, median SA · 0/2 roles measured
- PepSpecBench Yeast OOD subset, median SAS · 0/2 roles measured
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 benchmark. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
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.
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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-benchmark-pepspecbench
- areas
- proteins-complexes
- contexts
- research
- entity level
- suite
- version
- v1 (arXiv:2605.01945v1)
- task
- Peptide tandem mass spectrum (fragment intensity) prediction
- scope note
- Peptide length 6-40, precursor charge 1-6, PTMs UNIMOD 1, 4 and 35. In-domain: PROSPECT-Mini and MassIVE-KB-Mini, 500k/50k/50k spectra each. OOD: seven 20k-spectrum subsets over five species from ProteomeXchange (MaxQuant 1% FDR); zero-shot transfer.
- source locator
- Sections 3.1-3.3; Appendix C
- limitations
- Preprint; six models all retrained by the benchmark authors.
Related records
- part of: PepSpecBench A. thaliana OOD subset, median SA
- part of: PepSpecBench A. thaliana OOD subset, median SAS
- part of: PepSpecBench C. elegans OOD subset, median SA
- part of: PepSpecBench C. elegans OOD subset, median SAS
- part of: PepSpecBench E. coli OOD subsets (both sources aggregated), median SA
- part of: PepSpecBench E. coli OOD subsets (both sources aggregated), median SAS
- part of: PepSpecBench HeLa OOD subset, median SA
- part of: PepSpecBench HeLa OOD subset, median SAS
- part of: PepSpecBench MassIVE-KB-Mini test split, median PCC
- part of: PepSpecBench MassIVE-KB-Mini test split, median SA
- part of: PepSpecBench MassIVE-KB-Mini test split, median SAS
- part of: PepSpecBench PROSPECT-Mini test split, median PCC
- part of: PepSpecBench PROSPECT-Mini test split, median SA
- part of: PepSpecBench PROSPECT-Mini test split, median SAS
- part of: PepSpecBench Yeast OOD subset, median SA
- part of: PepSpecBench Yeast OOD subset, median SAS