{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T11:47:31Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 25.9, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a09570-8b94-7873-8129-14884c869c88\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: Orbitrap\nSense to describe: (none recorded)\nDomain code: PHY.OBJ\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 044: 1001 regist", "usd": 0.0, "recall": true }, "codex": { "seconds": 75.3, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a09570-8ba2-7b71-adaf-071fbc3dccfd\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: Orbitrap\nRegistry id: vr.tr.orbitrap\nPlane / domain: PHY / PHY.OBJ\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nContex" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:48:47+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:29+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q2607924", "registryId": "vr.tr.orbitrap", "name": "Orbitrap", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.OBJ" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q2607924/", "model": { "registry_id": "vr.tr.orbitrap", "name": "Orbitrap", "purpose": "Enable an AI agent to recognise an Orbitrap mass analyser, assess its measurement readiness, and select acquisition or maintenance actions supported by its configuration and condition.", "definition": "An Orbitrap is an electrostatic ion-trap mass analyzer that determines ion mass-to-charge ratios from the frequencies of axial oscillation of trapped ions, measured through image-current detection and Fourier transformation.", "scope_statement": "This model owns the Orbitrap electrostatic mass-analyser kind registered as vr.tr.orbitrap, including ion confinement, image-current detection, measurement performance and operating dependencies; product variants and individual units are linked instances.", "in_scope": [ "Electrode geometry and electrostatic confinement of orbiting ions", "Ion-packet admission and interfaces to upstream ion handling", "Axial-oscillation image-current acquisition and conversion to mass-to-charge spectra", "Resolving power, mass error and calibration evidence under stated acquisition conditions", "Analyser vacuum, electrical readiness, diagnostic state and service boundaries" ], "out_of_scope": [ "Complete mass-spectrometer product families and their commercial specifications", "Ion sources, chromatography systems and sample preparation", "Upstream quadrupoles, accumulation traps and fragmentation cells as independently modelled components", "Chemical identification, spectral-library interpretation and biological conclusions", "Individual instrument ownership, procurement and laboratory accreditation" ], "distinguishing_features": [ "Identify electrostatic confinement around a central electrode, with axial oscillation as the mass-measurement motion. [Manufacturer measuring principle](https://docs.thermofisher.com/r/Orbitrap-Astral-Operating-Manual/1780452107v2en-US)", "Verify that split outer electrodes sense an ion-induced image current used to determine axial frequencies and mass-to-charge ratios. [Primary research](https://pubs.acs.org/doi/10.1021/ac0258047)", "Distinguish the orbital electrostatic analyser from RF ion traps, time-of-flight analysers and Fourier-transform ion-cyclotron-resonance analysers. [Manufacturer technology overview](https://www.thermofisher.com/au/en/home/industrial/mass-spectrometry/mass-spectrometry-learning-center/mass-analyzer-technology-overview/mass-analyzer-technology-overview.html)", "Require evidence for the Orbitrap component inside a hybrid instrument; the presence of an upstream quadrupole or linear ion trap does not make those components Orbitrap analysers." ], "characteristics": [ { "name": "Analyser variant", "kind": "category", "unit_or_values": "Documented electrode or field variant; unknown", "why_it_matters": "Performance claims and operating limits must belong to the installed variant." }, { "name": "Host and ion-path interfaces", "kind": "relation", "unit_or_values": "Host instrument, ion accumulator, transfer optics and controller references", "why_it_matters": "Determines which preparation, injection and acquisition actions the host supports." }, { "name": "Acquisition mass-to-charge interval", "kind": "measurement", "unit_or_values": "Lower and upper m/z bounds, with charge and reporting convention recorded", "why_it_matters": "Establishes whether the intended ions fall within the configured measurement interval." }, { "name": "Resolving power", "kind": "measurement", "unit_or_values": "Dimensionless m/Δm, with peak-width convention, reference m/z and transient duration", "why_it_matters": "Makes resolution claims comparable and connects peak separation to acquisition conditions." }, { "name": "Measured mass error", "kind": "measurement", "unit_or_values": "Signed ppm against a named reference ion, with test conditions", "why_it_matters": "Shows whether current calibration supports the intended mass tolerance." }, { "name": "Detection transient duration", "kind": "measurement", "unit_or_values": "ms", "why_it_matters": "Supports assessment of resolving power and acquisition timing." }, { "name": "Ion population control", "kind": "category", "unit_or_values": "Host-supported target mode, target value convention and injection-time limit", "why_it_matters": "Makes population-dependent measurement behaviour assessable without treating a software target as a direct ion count." }, { "name": "Analyser-region pressure", "kind": "measurement", "unit_or_values": "Pa or mbar, with gauge location and reading status", "why_it_matters": "Allows comparison with the documented vacuum conditions required for operation." }, { "name": "Calibration status", "kind": "state", "unit_or_values": "Unverified; accepted within recorded limits; failed; invalidated", "why_it_matters": "Determines whether measurements can be accepted or require calibration and verification." }, { "name": "Operating readiness", "kind": "state", "unit_or_values": "Unavailable; pumping down; stabilising; ready; acquiring; fault; service", "why_it_matters": "Constrains permissible acquisition and service actions using actual host status." } ], "affordances": [ "Identify an installed Orbitrap analyser and link it to its host configuration and documentation.", "Select a supported m/z interval and resolution setting for a stated measurement requirement.", "Request acquisition through the host controller when calibration, vacuum and electrical conditions permit.", "Evaluate reference-ion measurements against explicit mass-error and resolving-power criteria.", "Investigate degraded spectra using ion-loading, transient, calibration and vacuum evidence.", "Route faults to documented recovery procedures or qualified service, then require measurement verification." ], "agent_conduct": { "may": [ "Operate and calibrate an Orbitrap instrument the agent is authorized to use.", "Process and report mass spectra with stated calibration, resolution and uncertainty." ], "must_not": [ "Report identifications beyond the confidence the data supports.", "Alter, delete or selectively omit spectra to change a result.", "Run samples for identifying people, such as forensic or clinical samples, outside an accredited process." ], "requires_human": [ "Releasing results used in clinical, forensic or regulatory decisions." ] }, "ethics": { "considerations": [ "Mass spectrometry results can decide prosecutions, diagnoses and product recalls.", "Data integrity and traceability protect people affected by those results." ], "affected_parties": [ "People whose samples are tested", "Researchers relying on the data" ] }, "owners": { "steward": "The laboratory that operates it.", "master_systems": [] }, "visual_identification": [ "A spindle-shaped central electrode inside a barrel-shaped outer electrode, enclosed in a high-vacuum mass spectrometer.", "Usually seen as a benchtop or floor instrument coupled to a chromatograph." ], "failure_modes_and_hazards": [ "High voltages and vacuum systems can injure untrained users.", "Poor calibration gives wrong identifications." ], "what_it_is_for": [ "This electrostatic mass analyzer is used in laboratory mass spectrometry to measure ion mass-to-charge ratios with high resolving power.", "It supports applications such as protein identification, metabolite characterization, environmental analysis and chemical quality control.", "It is commonly integrated with separation systems and other ion-handling components whose configuration determines the available measurements." ], "standards_and_regulation": [ "IEC 61010-1, issued by the International Electrotechnical Commission, specifies general safety requirements applicable to laboratory electrical equipment incorporating this analyzer.", "IEC 61326-1, issued by the International Electrotechnical Commission, specifies electromagnetic compatibility requirements applicable to electrical laboratory equipment incorporating this analyzer." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q2607924: Orbitrap", "url": "https://www.wikidata.org/wiki/Q2607924", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Orbitrap", "url": "https://en.wikipedia.org/wiki/Orbitrap", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "analyser-identity-and-boundary", "name": "Analyser identity and boundary", "description": "Establish what makes the registered thing an Orbitrap and where its responsibility ends.", "rationale": "Orbitrap names are also used in complete instrument names, which can obscure the analyser boundary.", "layers": [ { "id": "electrostatic-identity", "name": "Electrostatic identity", "description": "Recognise the confinement and detection architecture.", "findings": [ { "id": "orbitrap-recognition-evidence", "name": "Orbitrap recognition evidence", "description": "Record evidence identifying the electrostatic orbital analyser and its axial image-current measurement, rather than relying only on a product label.", "questions": [ { "text": "Which documented electrode and detection features establish that this component is an Orbitrap?", "kind": "definition", "id": "orbitrap-recognition-evidence-q01" }, { "text": "Which manufacturer document or component record supports that identification?", "kind": "provenance", "id": "orbitrap-recognition-evidence-q02" } ] } ] }, { "id": "host-component-boundary", "name": "Host component boundary", "description": "Separate the analyser from the surrounding hybrid mass spectrometer.", "findings": [ { "id": "installed-configuration", "name": "Installed configuration", "description": "Link the analyser variant to the host, upstream ion handling and control system without importing their complete capabilities.", "questions": [ { "text": "Does the available name identify an analyser kind, a host product variant or an individual instrument?", "kind": "boundary", "id": "installed-configuration-q01" }, { "text": "Which ion-selection, accumulation and fragmentation functions belong to neighbouring components?", "kind": "boundary", "id": "installed-configuration-q02" } ] } ] } ] }, { "id": "ion-admission-and-confinement", "name": "Ion admission and confinement", "description": "Describe how a suitable ion population enters and remains measurable in the analyser.", "rationale": "Injection conditions and ion population connect upstream preparation to usable Orbitrap signals.", "layers": [ { "id": "ion-packet-interface", "name": "Ion-packet interface", "description": "Record the supported transfer path and admission conditions.", "findings": [ { "id": "injection-compatibility", "name": "Injection compatibility", "description": "Treat packet preparation and injection as configuration-dependent interfaces requiring host documentation.", "questions": [ { "text": "Which component prepares the ion packet, and which supported path admits it to this analyser?", "kind": "boundary", "id": "injection-compatibility-q01" }, { "text": "Which m/z, polarity and injection settings are supported for that path?", "kind": "measurement", "id": "injection-compatibility-q02" } ] } ] }, { "id": "population-and-field-control", "name": "Population and field control", "description": "Connect loading and electrical conditions to stable measurement.", "findings": [ { "id": "population-operating-envelope", "name": "Population operating envelope", "description": "Record population-control settings and evidence of loading-dependent degradation without assuming universal targets.", "questions": [ { "text": "What population target and injection-time limit were used, and what do their reported values mean?", "kind": "measurement", "id": "population-operating-envelope-q01" }, { "text": "Which diagnostics or reference measurements justify changing ion loading or stopping acquisition?", "kind": "action", "id": "population-operating-envelope-q02" } ] } ] } ] }, { "id": "transient-and-spectrum", "name": "Transient and spectrum", "description": "Connect the measured image-current transient to the reported mass spectrum.", "rationale": "Acquisition duration and signal processing are necessary context for interpreting an Orbitrap result.", "layers": [ { "id": "image-current-acquisition", "name": "Image-current acquisition", "description": "Record the duration and quality of the axial-oscillation signal.", "findings": [ { "id": "transient-evidence", "name": "Transient evidence", "description": "Associate each spectrum with available transient settings, signal diagnostics and acquisition timing.", "questions": [ { "text": "What detection duration produced the spectrum, and is that value measured or inferred from a setting?", "kind": "measurement", "id": "transient-evidence-q01" }, { "text": "Which available diagnostics indicate inadequate signal, excessive decay or an acquisition fault?", "kind": "measurement", "id": "transient-evidence-q02" } ] } ] }, { "id": "frequency-to-mass-processing", "name": "Frequency-to-mass processing", "description": "Preserve the processing and calibration context of spectral values.", "findings": [ { "id": "spectrum-processing-lineage", "name": "Spectrum processing lineage", "description": "Link reported peaks to processing software, calibration and output representation.", "questions": [ { "text": "Which software version, processing options and calibration converted the frequency signal into m/z values?", "kind": "provenance", "id": "spectrum-processing-lineage-q01" }, { "text": "Are the retained results raw transients, profile spectra or centroid peaks, and what information is unavailable?", "kind": "boundary", "id": "spectrum-processing-lineage-q02" } ] } ] } ] }, { "id": "measurement-fitness", "name": "Measurement fitness", "description": "Judge whether current analyser performance supports a particular measurement.", "rationale": "A nominal resolution setting or product specification does not establish current measurement quality.", "layers": [ { "id": "resolution-and-timing", "name": "Resolution and timing", "description": "Evaluate peak separation together with acquisition timing.", "findings": [ { "id": "qualified-resolving-power", "name": "Qualified resolving power", "description": "Record resolving power with reference m/z, width convention and acquisition conditions.", "questions": [ { "text": "What resolving power was demonstrated at the relevant m/z, using which peak-width convention?", "kind": "measurement", "id": "qualified-resolving-power-q01" }, { "text": "Which supported acquisition setting satisfies both the required peak separation and sampling interval?", "kind": "action", "id": "qualified-resolving-power-q02" } ] } ] }, { "id": "mass-calibration-and-verification", "name": "Mass calibration and verification", "description": "Assess calibration using traceable reference measurements.", "findings": [ { "id": "calibration-acceptance", "name": "Calibration acceptance", "description": "Separate completion of calibration from evidence that measurements meet the required error limits.", "questions": [ { "text": "Which reference ions, calibration mode, timestamp and acceptance limits support the current status?", "kind": "provenance", "id": "calibration-acceptance-q01" }, { "text": "What mass errors were measured across the relevant m/z interval and operating conditions?", "kind": "measurement", "id": "calibration-acceptance-q02" } ] } ] } ] }, { "id": "operating-readiness-and-recovery", "name": "Operating readiness and recovery", "description": "Determine whether the analyser can operate and how degraded performance should be handled.", "rationale": "Orbitrap measurements depend on the host's vacuum, electrical control and authorised service procedures.", "layers": [ { "id": "vacuum-and-electrical-readiness", "name": "Vacuum and electrical readiness", "description": "Connect analyser-region conditions and host interlocks to permitted actions.", "findings": [ { "id": "acquisition-permission-evidence", "name": "Acquisition permission evidence", "description": "Use documented readiness conditions and actual controller status to determine whether acquisition is permitted.", "questions": [ { "text": "What analyser-region pressure, voltage status and stabilisation conditions does this configuration require?", "kind": "measurement", "id": "acquisition-permission-evidence-q01" }, { "text": "Which host interlocks or fault states prevent injection or analyser operation?", "kind": "action", "id": "acquisition-permission-evidence-q02" } ] } ] }, { "id": "fault-localisation-and-service", "name": "Fault localisation and service", "description": "Distinguish analyser faults from upstream problems and establish recovery evidence.", "findings": [ { "id": "degradation-response", "name": "Degradation response", "description": "Relate signal loss, peak broadening or mass drift to diagnostic evidence, documented interventions and post-service checks.", "questions": [ { "text": "What evidence localises degradation to the analyser rather than the source, transfer path or data processing?", "kind": "boundary", "id": "degradation-response-q01" }, { "text": "Which recovery steps are operator-permitted, which require service, and what verification is required before reuse?", "kind": "action", "id": "degradation-response-q02" } ] } ] } ] }, { "id": "evidence-and-external-alignment", "name": "Evidence and external alignment", "description": "What the world already says about this thing, gathered so the model can be checked against it.", "rationale": "A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.", "layers": [ { "id": "reported-evidence", "name": "Reported evidence", "description": "Findings from the breadth pass, kept separate from the structural claims.", "findings": [ { "id": "evidence-confidence-notes", "name": "Check these first", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "This is recalled knowledge without source verification; Orbitrap also appears in branded instrument-family names, so the registry should distinguish analyzer type from complete products.", "Resolving power depends on mass-to-charge ratio and transient duration; numerical ranges are representative rather than universal specifications.", "Safety-standard applicability and compliance must be checked for the particular complete instrument and jurisdiction." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of Orbitrap this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-kinds", "name": "Kinds and varieties", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Conventional Orbitrap analyzer", "High-field Orbitrap analyzer" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of Orbitrap this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-standards-and-regulation", "name": "Standards and regulation", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "IEC 61010-1, issued by the International Electrotechnical Commission, provides general safety requirements for electrical measurement, control and laboratory equipment and is relevant to complete Orbitrap mass spectrometers." ], "questions": [ { "id": "evidence-standards-and-regulation-q01", "text": "Which of these standards and regulation hold for the sense of Orbitrap this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-real-world-use", "name": "Real-world use", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Identification and quantification of proteins and peptides in proteomics", "Metabolomics and lipidomics", "Pharmaceutical compound characterization and impurity analysis", "Screening for contaminants in food and environmental samples", "Accurate-mass measurements supporting elemental-composition assignment" ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of Orbitrap this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-measurements", "name": "Typical measurements", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "quantity": "Mass resolving power, m/Δm at full width at half maximum", "typical_range": "Approximately 60,000-500,000 at m/z 200, depending on analyzer generation and acquisition settings", "unit": "dimensionless" }, { "quantity": "Mass measurement error under suitable calibration and operating conditions", "typical_range": "Often within ±1-5", "unit": "ppm" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of Orbitrap this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-failure-modes-and-hazards", "name": "Failure modes and hazards", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Excessive trapped-ion populations cause space-charge effects that can shift measured frequencies and degrade performance.", "Poor vacuum increases ion collisions, shortening usable transients and reducing sensitivity or resolving power.", "Electrode contamination or charging can distort the trapping field and degrade performance.", "Calibration drift can produce systematic mass errors.", "High-voltage electrodes and associated electronics present electrical hazards during servicing of the complete instrument." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of Orbitrap this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-neighbours", "name": "Neighbouring kinds and how to tell them apart", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "name": "Orbitrap mass spectrometer", "difference": "The complete instrument includes an ion source, ion-transfer components, vacuum system and electronics; the Orbitrap itself is its mass analyzer." }, { "name": "Fourier-transform ion cyclotron resonance mass analyzer", "difference": "Both use frequency-domain image-current detection, but FT-ICR measures ion cyclotron motion in a magnetic field, whereas an Orbitrap measures axial motion in an electrostatic field." }, { "name": "Quadrupole mass analyzer", "difference": "A quadrupole ordinarily selects ions through stability of trajectories in combined radio-frequency and static electric fields rather than measuring axial oscillation frequencies." }, { "name": "Time-of-flight mass analyzer", "difference": "A time-of-flight analyzer determines mass-to-charge ratio from ion flight times rather than trapped-ion oscillation frequencies." }, { "name": "Radio-frequency ion trap", "difference": "A radio-frequency ion trap uses time-varying fields for confinement; an Orbitrap uses a static electrostatic field and injected ion motion." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of Orbitrap this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the registry intend Orbitrap specifically as the analyser kind, or as a broader branded instrument category? This draft adopts the analyser boundary.", "Which authoritative variant documents establish applicable m/z limits, resolving-power conditions, dimensions, voltage requirements and vacuum thresholds?", "Which ion-loading controls, transient diagnostics and calibration records are exposed by each supported host controller?", "Which experimentally supported criteria distinguish population effects, vacuum degradation, electrode contamination and processing artefacts in the intended configurations?", "Which maintenance procedures, consumables, interlocks and issuing-body standards apply to the analyser itself, and which belong exclusively to the complete host instrument?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 17, "questions": 27 } }