BEMO:2000375 · BEMO metric v1.0.0

Peptide-Spectrum Match Quality

A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of peptide-spectrum match quality.

CandidateOperationalDefinitionRequiredContextSpecificProtocolRequired
Scientific pillar
Genetics, Omics, and Systems Biology
Source category
Proteomics and Metabolomics
Output scale
ContextDependentMixedScale
Source maturity
Established

Scientific meaning

What it measures

Assesses peptide-spectrum match quality using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.

Why it matters

Material weakness in peptide-spectrum match quality can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.

Measurement criteria

Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.

Typical methods of assessment

Target-decoy analysis; spectral scoring; reference standards; replicate injections; retention-time and mass-error monitoring; orthogonal confirmation.

Computation profile

Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.
Computation mode
ContextSpecificMetricComputation
Readiness
OperationalDefinitionRequired
Formula status
ContextSpecificProtocolRequired
Method family
metric-specific quantitative or qualitative assessment
Output datatype
xsd:anySimpleType
Unit or scale
Metric-specific continuous, categorical, or ordinal scale
Numeric range
Context dependent
Directionality
ContextDependentDirection

Required inputs

  • evidence_records
  • assessment_context
  • operational_definition
  • computation_protocol_version

Optional inputs

  • weights
  • thresholds
  • reference_standard
  • expert_adjudication

Machine-readable expression

{
  "language": "BEMO-Expression-JSON",
  "operator": "external_protocol",
  "protocolRef": "REQUIRED"
}

Computation policies

Aggregation
Not specified in source; must be defined and versioned before composite use.
Normalization
None by default; any normalization must be justified, versioned, and validated.
Missing data
Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.
Uncertainty required
Yes
Uncertainty method
Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.
Confidence interval required
Yes
Threshold policy
Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.
Decision thresholds
No universal threshold declared
Quality control
Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.
Calibration
As applicable; mandatory for probabilistic or normalized outputs.

Applicability and validation

Evidence object
Result / experiment / study / body of evidence, as applicable
Evidence level
Result / experiment / study / body of evidence, as applicable
Study types
Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies
Domain
Proteomics and Metabolomics
Required data sources
Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.
Validation status
Source maturity: Established; BEMO computation profile requires independent validation.
Benchmark
A representative, versioned benchmark set is required before production use.
Reference standard
Use an independent reference standard when one exists; document expert-adjudicated alternatives.
External validation required
Yes

Interpretation safeguards

Common misinterpretations

Treating peptide-spectrum match quality as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.

Limitations

Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.

Dependency status

Not yet curated. Closely related metrics are represented; causal or computational dependencies require expert curation.

Source provenance

Source workbook
Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx
Source worksheet
Biomedical Evidence Metrics
Source row
382
Source record SHA-256
69f7898b8265a7daaa45bd90d4d5387c92da6521721d3c4901a5c208a63f0169
Definition source
Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 382; see source_references

Scientific references (3)

  1. https://www.psidev.info/miapeSource framework, standard, guideline, or originSource-preserved; URL reachability not asserted by this package
  2. https://www.psidev.info/Source framework, standard, guideline, or originSource-preserved; URL reachability not asserted by this package
  3. https://www.metabolomics-msi.org/Source framework, standard, guideline, or originSource-preserved; URL reachability not asserted by this package

Governance and FAIR status

Lifecycle
Candidate
Approval
Draft
Owner
BEMO Project
Curator
Unassigned
Reviewer
Unassigned
License
Pending owner approval; CC BY 4.0 recommended for OBO compatibility.
Findable
Provisional: stable local ID assigned; public namespace registration pending.
Accessible
Provisional: package is distributable; permanent public release location pending.
Interoperable
Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.
Reusable
Provisional: rich metadata supplied; open-license owner approval pending.
Governance note
Candidate term pending scientific, ontology-engineering, and computation-method review.
Editor note
Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.