{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.orbitrap","code":"thing-q2607924","url":"https://ver.cy/models/thing/q2607924/","name":"Orbitrap","alternateNames":[],"kind":"thing","status":"published","version":"0.1.0-research.1","language":"en","classifiers":{"family":"Thing Registry","category":"Physical world and living systems","entryKind":"thing","plane":"PHY","domain":["PHY.OBJ"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"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.","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.","scope":{"in":["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":["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"],"boundaries":[]},"distinguishingFeatures":["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."],"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.","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?","id":"orbitrap-recognition-evidence-q01","kind":"definition"},{"text":"Which manufacturer document or component record supports that identification?","id":"orbitrap-recognition-evidence-q02","kind":"provenance"}]}]},{"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?","id":"installed-configuration-q01","kind":"boundary"},{"text":"Which ion-selection, accumulation and fragmentation functions belong to neighbouring components?","id":"installed-configuration-q02","kind":"boundary"}]}]}]},{"id":"ion-admission-and-confinement","name":"Ion admission and confinement","description":"Describe how a suitable ion population enters and remains measurable in the analyser.","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?","id":"injection-compatibility-q01","kind":"boundary"},{"text":"Which m/z, polarity and injection settings are supported for that path?","id":"injection-compatibility-q02","kind":"measurement"}]}]},{"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?","id":"population-operating-envelope-q01","kind":"measurement"},{"text":"Which diagnostics or reference measurements justify changing ion loading or stopping acquisition?","id":"population-operating-envelope-q02","kind":"action"}]}]}]},{"id":"transient-and-spectrum","name":"Transient and spectrum","description":"Connect the measured image-current transient to the reported mass spectrum.","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?","id":"transient-evidence-q01","kind":"measurement"},{"text":"Which available diagnostics indicate inadequate signal, excessive decay or an acquisition fault?","id":"transient-evidence-q02","kind":"measurement"}]}]},{"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?","id":"spectrum-processing-lineage-q01","kind":"provenance"},{"text":"Are the retained results raw transients, profile spectra or centroid peaks, and what information is unavailable?","id":"spectrum-processing-lineage-q02","kind":"boundary"}]}]}]},{"id":"measurement-fitness","name":"Measurement fitness","description":"Judge whether current analyser performance supports a particular measurement.","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?","id":"qualified-resolving-power-q01","kind":"measurement"},{"text":"Which supported acquisition setting satisfies both the required peak separation and sampling interval?","id":"qualified-resolving-power-q02","kind":"action"}]}]},{"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?","id":"calibration-acceptance-q01","kind":"provenance"},{"text":"What mass errors were measured across the relevant m/z interval and operating conditions?","id":"calibration-acceptance-q02","kind":"measurement"}]}]}]},{"id":"operating-readiness-and-recovery","name":"Operating readiness and recovery","description":"Determine whether the analyser can operate and how degraded performance should be handled.","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?","id":"acquisition-permission-evidence-q01","kind":"measurement"},{"text":"Which host interlocks or fault states prevent injection or analyser operation?","id":"acquisition-permission-evidence-q02","kind":"action"}]}]},{"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?","id":"degradation-response-q01","kind":"boundary"},{"text":"Which recovery steps are operator-permitted, which require service, and what verification is required before reuse?","id":"degradation-response-q02","kind":"action"}]}]}]},{"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.","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.","questions":[{"text":"Which of these check these first hold for the sense of Orbitrap this model covers, and on what evidence?","id":"evidence-confidence-notes-q01","kind":"provenance"}]},{"id":"evidence-kinds","name":"Kinds and varieties","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these kinds and varieties hold for the sense of Orbitrap this model covers, and on what evidence?","id":"evidence-kinds-q01","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.","questions":[{"text":"Which of these standards and regulation hold for the sense of Orbitrap this model covers, and on what evidence?","id":"evidence-standards-and-regulation-q01","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.","questions":[{"text":"Which of these real-world use hold for the sense of Orbitrap this model covers, and on what evidence?","id":"evidence-real-world-use-q01","kind":"provenance"}]},{"id":"evidence-measurements","name":"Typical measurements","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these typical measurements hold for the sense of Orbitrap this model covers, and on what evidence?","id":"evidence-measurements-q01","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.","questions":[{"text":"Which of these failure modes and hazards hold for the sense of Orbitrap this model covers, and on what evidence?","id":"evidence-failure-modes-and-hazards-q01","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.","questions":[{"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?","id":"evidence-neighbours-q01","kind":"provenance"}]}]}]}]},"agentConduct":{"may":["Operate and calibrate an Orbitrap instrument the agent is authorized to use.","Process and report mass spectra with stated calibration, resolution and uncertainty."],"mustNot":["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."],"requiresHuman":["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."],"affectedParties":["People whose samples are tested","Researchers relying on the data"]},"owners":{"steward":"The laboratory that operates it.","roles":[],"masterSystems":[]},"relations":[{"target":"Q114909379","type":"parent","note":"registry parent class"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.orbitrap","Wikidata: Q2607924 (https://www.wikidata.org/wiki/Q2607924)"]},"properties":{"applicability":"required","items":["Analyser variant: Documented electrode or field variant; unknown","Host and ion-path interfaces: Host instrument, ion accumulator, transfer optics and controller references","Acquisition mass-to-charge interval: Lower and upper m/z bounds, with charge and reporting convention recorded","Resolving power: Dimensionless m/Δm, with peak-width convention, reference m/z and transient duration","Measured mass error: Signed ppm against a named reference ion, with test conditions","Detection transient duration: ms","Ion population control: Host-supported target mode, target value convention and injection-time limit","Analyser-region pressure: Pa or mbar, with gauge location and reading status","Calibration status: Unverified; accepted within recorded limits; failed; invalidated","Operating readiness: Unavailable; pumping down; stabilising; ready; acquiring; fault; service"]},"recognition":{"applicability":"required","items":["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."]},"capabilities":{"applicability":"required","items":["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."]},"hazards":{"applicability":"required","items":["High voltages and vacuum systems can injure untrained users.","Poor calibration gives wrong identifications."]},"interfaces":{"applicability":"required","items":["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."]},"context":{"applicability":"required","items":["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."]}},"sources":[{"title":"Wikidata item Q2607924: Orbitrap","url":"https://www.wikidata.org/wiki/Q2607924","note":"identity and sense of the item"},{"title":"Wikipedia: Orbitrap","url":"https://en.wikipedia.org/wiki/Orbitrap","note":"general description of the item"}],"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?"],"resources":{"spec":"/models/things/publications/thing-q2607924/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q2607924/spec.json"],"providers":["Codex"],"researchStatus":"unreviewed","generatedAt":"2026-09-12T11:47:31Z","builder":"tools/build_cards.py@1.0.0"},"completeness":{"sections":{"classifiers":"filled","whatItIs":"filled","purpose":"filled","distinguishingFeatures":"filled","structure":"filled","agentConduct":"filled","ethics":"filled","owners":"filled","relations":"filled","interaction.identity":"filled","interaction.properties":"filled","interaction.recognition":"filled","interaction.capabilities":"filled","interaction.hazards":"filled","interaction.interfaces":"filled","interaction.context":"filled","sources":"filled"},"notes":{"_gate":"Published through the thing publication gate 1.0 on 2026-10-07T10:10:29+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass"},"score":1.0}}