Thermo Orbitrap (Instrument API)
PYPI · LABMCP-THERMO-IAPI · SCANNED SEP 30
MCP server adapter for Thermo Fisher Orbitrap mass spectrometers via the licensed Instrument API.
Available components
How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. How we score → Why this is hard to score →
Supply Chain Security99
- No malware found by supply-chain analysis.Pass
- No known CVEs affecting this package version or its production dependencies.Pass
- Runs hatchling.build at install time, a recognised build step with no custom scripting around it. View diagnostics → Pass
- 2 of 17 dependencies flagged as unhealthy. View diagnostics → Partial
Provenance & Transparency100
- Source repository is publicly reachable at the declared URL. View diagnostics → Pass
- Cryptographically verified build provenance (signed, bound to K-Dense-AI/lab-instrument-mcps). View diagnostics → Pass
- Clear OSI-approved license (Apache-2.0).Pass
- Actively maintained (last published 3 days ago).Pass
- Publishes a security disclosure policy (SECURITY.md).Pass
Schema Quality & AI Usability74
- AI-judged instruction clarity (excellent).Pass
- Context-footprint check failed: tool/resource definitions use about 2116 tokens (~141/item across 15 items; 15 tools + 0 resources), over budget; trim descriptions and params. See how to fix → Fail
- Usage-examples check failed: none of the tools include examples. See how to fix → Fail
Stability & Change Management13
- Stability observed for 4 of 30 days with no destabilising changes; credit accrues until the full window elapses.Partial
Tool Coverage97
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 91% of tool parameters carry a description.Partial
- Structured output schemas are declared (100% of tools); any adoption earns full credit.Pass
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 15 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 16 captured unit(s) of tool text and found none that tries to manipulate the model reading it.Pass
Capabilities100
- Implements a current MCP spec version (2026-07-28).Pass
How do I install the Thermo Orbitrap (Instrument API) MCP server?
Thermo Orbitrap (Instrument API) runs locally as a PyPI package, launched with uvx labmcp-thermo-iapi. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.
pypi · labmcp-thermo-iapi
claude mcp add k-dense-ai-labmcp-thermo-iapi -- uvx labmcp-thermo-iapi
{
"mcpServers": {
"k-dense-ai-labmcp-thermo-iapi": {
"command": "uvx",
"args": [
"labmcp-thermo-iapi"
]
}
}
} {
"servers": {
"k-dense-ai-labmcp-thermo-iapi": {
"command": "uvx",
"args": [
"labmcp-thermo-iapi"
]
}
}
} codex mcp add k-dense-ai-labmcp-thermo-iapi -- uvx labmcp-thermo-iapi
{
"$schema": "https://opencode.ai/config.json",
"mcp": {
"k-dense-ai-labmcp-thermo-iapi": {
"type": "local",
"command": [
"uvx",
"labmcp-thermo-iapi"
],
"enabled": true
}
}
} openclaw mcp add k-dense-ai-labmcp-thermo-iapi --command uvx --arg labmcp-thermo-iapi
mcp_servers:
k-dense-ai-labmcp-thermo-iapi:
command: "uvx"
args: ["labmcp-thermo-iapi"] {
"McpServers": {
"k-dense-ai-labmcp-thermo-iapi": {
"Transport": "stdio",
"Command": "uvx",
"Arguments": [
"labmcp-thermo-iapi"
]
}
}
} assistant mcp add k-dense-ai-labmcp-thermo-iapi -t stdio -c uvx -a labmcp-thermo-iapi
{
"mcpServers": {
"k-dense-ai-labmcp-thermo-iapi": {
"command": "uvx",
"args": [
"labmcp-thermo-iapi"
]
}
}
} Every change we have recorded for this component, newest first. Security-relevant changes are always shown. ▲ marks a change for the better, ▼ a change for the worse; unmarked changes are neutral.
- 30 Sept 26 +16
- Malware scan: unverified → pass ▲ security
- 29 Sept 26 −15
- Malware scan: pass → unverified ▼ security
- 28 Sept 26 +43
- We updated how we score, so this day's move reflects our rubric, not a change to the server See what changed → functional
- 27 Sept 26 −31
- Tool safety: pass → unverified ▼ security
- Stability: Stability not yet verified: we do not have a sandbox capture of the MCP schema this version of the package serves yet. security
- Capabilities: pass → unverified ▼ functional
- Tool coverage: 100 → unverified ▼ functional
- First check of Schema quality: unverified functional
- Package version: 0.1.0 → 0.1.1 functional
- 26 Sept 26 70
First indexed and scored.
Diagnostic detail from the automated scan of this channel: what the scanner observed at each step, so you can see exactly where a check passed or failed. It is informational only and never changes the trust score.
Captured 30 Sept 2026 · Analysed pypi/labmcp-thermo-iapi@0.1.1
Provenance Verified
A signed build attestation was found and verified, binding this exact artifact to the source repository it claims to come from.
| Result | Verified |
|---|---|
| Ecosystem | pypi |
| Reason | Verified |
| Discovered via | Registry attestation endpoint |
| Source repo | K-Dense-AI/lab-instrument-mcps |
| Certificate issuer | https://token.actions.githubusercontent.com |
| Certificate SAN | https://github.com/K-Dense-AI/lab-instrument-mcps/.github/workflows/release.yml@refs/tags/labmcp-thermo-iapi-v0.1.1 |
| Rekor log index | 2969517776 |
| Predicate type | PyPI publish attestation https://docs.pypi.org/attestations/publish/v1 |
| Subject digest | sha256:f58a3d7e97e35bf5a31e46e81bf15d74c5882ef3d5644ab9b36471a62e984b0b |
Background: How many MCP packages publish verified provenance →
Install scripts 1 script
| Hook | Tier | Command |
|---|---|---|
| build_backend | allowlisted | hatchling.build |
Background: Why install scripts are a supply-chain risk →
Dependencies 17 packages
| Packages resolved | 17 |
|---|---|
| Stale | 2 |
| Tree resolution | Complete |
Background: SBOMs and build attestations, explained →
The tools this component advertises to a client, with an estimated token cost for each. Expand a tool to see its parameters and schema. The per-tool counts are indicative and are not scored directly; the schema's total context footprint is one signal in Schema Quality & AI Usability. A tool's description is untrusted text the model reads on every call, which is what makes this list a security surface and not just an inventory: how tool poisoning works →
cancel_custom_scans Cancel Custom Scans ~26
Cancel any pending custom scan and its processing delay (IAPI CancelCustomScan).
Input schema present but exposes no named parameters.
| Name | Type | Req | Description |
|---|---|---|---|
| result | string | yes | – |
No examples provided.
cancel_repeating_scan Cancel Repeating Scan ~27
Cancel the repeating scan set with set_repeating_scan (IAPI CancelRepetition).
Input schema present but exposes no named parameters.
| Name | Type | Req | Description |
|---|---|---|---|
| result | string | yes | – |
No examples provided.
get_command_log Get Command Log ~46
Return the most recent raw commands sent to / replies received from the instrument (newest last). Useful for debugging and for recording what was done.
| Name | Type | Req | Description |
|---|---|---|---|
| limit | integer | – | – |
| Name | Type | Req | Description |
|---|---|---|---|
| result | array | yes | – |
No examples provided.
get_connection_info Get Connection Info ~40
Report which instrument is connected (identity, address, simulated or real), whether the server is read-only, and the active safety limits. Call this first.
Input schema present but exposes no named parameters.
Structured output declared, but exposes no named fields.
No examples provided.
get_instrument_status Get Instrument Status ~85
Report the instrument model, IAPI service/instrument connection, system mode and state (On/Standby/Off; Running/ReadyToDownload/...), whether an acquisition can be paused or resumed, the IAPI licence where the API exposes it, requested readbacks, the latest scan status log (vacuum, source) and how many scans have arrived.
Input schema present but exposes no named parameters.
| Name | Type | Req | Description |
|---|---|---|---|
| acquiring | boolean | yes | – |
| acquisition | – | – | – |
| api_license | – | yes | IAPI licence found (Exploris only; None = not queryable) |
| backend | string | yes | – |
| can_pause | boolean | yes | – |
| can_resume | boolean | yes | – |
| custom_scans_last_minute | integer | yes | – |
| family | – | yes | – |
| instrument_connected | boolean | yes | – |
| last_scan_at | – | yes | – |
| last_status_log | object | yes | Latest scan status log (vacuum, source, ...) |
| model | string | yes | – |
| readback_names | array | yes | Instrument value names the API exposes |
| readbacks | object | yes | Requested instrument values (IInstrumentValues) |
| scans_received | integer | yes | – |
| service_connected | boolean | yes | – |
| system_mode | – | yes | IState.SystemMode, e.g. On, Standby, Off, Disconnected |
| system_state | – | yes | IState.SystemState, e.g. Running, ReadyToDownload, Error |
| timestamp | string | yes | – |
No examples provided.
get_possible_scan_parameters Get Possible Scan Parameters ~82
List the scan parameters this instrument accepts for custom and repeating scans (IScans.PossibleParameters): name, allowed range or choices, default and help. The set depends on the model, licence and Tune version.
| Name | Type | Req | Description |
|---|---|---|---|
| name_contains | – | – | Case-insensitive name filter |
| refresh | boolean | – | Re-read from the instrument instead of the cache |
| Name | Type | Req | Description |
|---|---|---|---|
| result | array | yes | – |
No examples provided.
get_recent_scans Get Recent Scans ~174
Return the most recent scans received from the instrument (oldest first), optionally only one MS order or one custom scan's access id: scan number, MS order, precursor m/z, AGC target, injection time and the most intense centroids. Scans only arrive in On mode.
| Name | Type | Req | Description |
|---|---|---|---|
| access_id | – | – | Only scans with this access id (-1 = system scans) |
| count | integer | – | Number of most recent matching scans |
| include_header_trailer | boolean | – | Include the raw header and trailer |
| max_centroids | integer | – | Most intense centroids to return per scan |
| ms_order | – | – | Only scans of this MS order (1 = MS1) |
| save_path | – | – | Optional .csv path (must not exist yet): write all kept centroids of the returned scans |
| Name | Type | Req | Description |
|---|---|---|---|
| buffered_total | integer | yes | – |
| returned | integer | yes | – |
| saved_to | – | – | – |
| scans | array | yes | – |
| timestamp | string | yes | – |
No examples provided.
pause_acquisition Pause Acquisition ~28
Pause the running acquisition (IAPI Pause). Fails if the instrument reports it cannot pause.
Input schema present but exposes no named parameters.
| Name | Type | Req | Description |
|---|---|---|---|
| result | string | yes | – |
No examples provided.
reconnect Reconnect ~35
Close and re-open the connection to the instrument (e.g. after it was power cycled or a cable was re-plugged).
Input schema present but exposes no named parameters.
Structured output declared, but exposes no named fields.
No examples provided.
resume_acquisition Resume Acquisition ~22
Resume a paused acquisition (IAPI Resume). Sample consumption continues.
Input schema present but exposes no named parameters.
| Name | Type | Req | Description |
|---|---|---|---|
| result | string | yes | – |
No examples provided.
set_repeating_scan Set Repeating Scan ~304
Define or replace the scan the instrument repeats when no method or custom scan is running (IAPI CreateRepeatingScan/SetRepetitionScan). Values are validated like submit_custom_scan. Cancel with cancel_repeating_scan.
| Name | Type | Req | Description |
|---|---|---|---|
| activation_type | – | – | ActivationType, e.g. HCD or CID |
| agc_target | – | – | AGCTarget (charges) |
| analyzer | – | – | Mass analyzer, e.g. Orbitrap or IonTrap (Tribrid) |
| collision_energy | – | – | CollisionEnergy (normalized, %) |
| extra_parameters | – | – | Other IAPI scan values by exact name (see get_possible_scan_parameters) |
| first_mass_mz | – | – | FirstMass: scan range start (m/z) |
| isolation_width_mz | – | – | IsolationWidth (m/z) |
| last_mass_mz | – | – | LastMass: scan range end (m/z) |
| max_injection_time_ms | – | – | MaxIT: maximum injection time (ms) |
| microscans | – | – | – |
| orbitrap_resolution | – | – | OrbitrapResolution at m/z 200; must be an allowed value |
| polarity | – | – | Polarity as the instrument lists it |
| precursor_mz | – | – | PrecursorMass (m/z) for MSn/SIM |
| running_number | – | – | Reported back as access_id (default: auto) |
| scan_description | – | – | ScanDescription stored with the scan |
| scan_type | – | – | ScanType, e.g. Full, SIM or MSn |
| Name | Type | Req | Description |
|---|---|---|---|
| custom_scans_last_minute | – | – | – |
| message | string | yes | – |
| running_number | integer | yes | – |
| sent | boolean | yes | True if IAPI reports the command was sent to the instrument |
| values | object | yes | The exact IAPI scan values sent |
No examples provided.
start_acquisition Start Acquisition ~157
Start an acquisition with the instrument's current settings (IAPI StartAcquisition), recording to a raw file. This consumes sample. The instrument must be On; an acquisition must not already be running. Stop it with stop_acquisition. scan_count and until_stopped acquisitions are cancelled automatically after max_acquisition_duration_s.
| Name | Type | Req | Description |
|---|---|---|---|
| comment | – | – | – |
| duration_s | – | – | For mode=duration |
| mode | string | yes | Stop after duration_s, after scan_count scans, or only when stopped |
| raw_file_path | – | – | Raw file to write on the instrument PC, e.g. D:\Data\run1.raw |
| sample_name | – | – | – |
| scan_count | – | – | For mode=scan_count |
| Name | Type | Req | Description |
|---|---|---|---|
| result | string | yes | – |
No examples provided.
stop_acquisition Stop Acquisition ~94
Stop the running acquisition (IAPI CancelAcquisition), by default also cancelling custom and repeating scans, and optionally switch the instrument to Standby (switch back to On in Tune). Every step is attempted even if an earlier one fails; failures are reported.
| Name | Type | Req | Description |
|---|---|---|---|
| cancel_scans | boolean | – | Also cancel pending custom scans and the repeating scan |
| standby | boolean | – | Then put the instrument in Standby |
| Name | Type | Req | Description |
|---|---|---|---|
| result | string | yes | – |
No examples provided.
submit_custom_scan Submit Custom Scan ~348
Place one custom scan to run next (IAPI CreateCustomScan/SetCustomScan); unset values fall back to the instrument's defaults. Every value is checked against PossibleParameters and the safety limits, and calls are rate-limited, before anything is sent. Fetch the result with wait_for_scan(access_id=running_number).
| Name | Type | Req | Description |
|---|---|---|---|
| activation_type | – | – | ActivationType, e.g. HCD or CID |
| agc_target | – | – | AGCTarget (charges) |
| analyzer | – | – | Mass analyzer, e.g. Orbitrap or IonTrap (Tribrid) |
| collision_energy | – | – | CollisionEnergy (normalized, %) |
| extra_parameters | – | – | Other IAPI scan values by exact name (see get_possible_scan_parameters) |
| first_mass_mz | – | – | FirstMass: scan range start (m/z) |
| isolation_width_mz | – | – | IsolationWidth (m/z) |
| last_mass_mz | – | – | LastMass: scan range end (m/z) |
| max_injection_time_ms | – | – | MaxIT: maximum injection time (ms) |
| microscans | – | – | – |
| orbitrap_resolution | – | – | OrbitrapResolution at m/z 200; must be an allowed value |
| polarity | – | – | Polarity as the instrument lists it |
| precursor_mz | – | – | PrecursorMass (m/z) for MSn/SIM |
| running_number | – | – | Reported back as access_id (default: auto) |
| scan_description | – | – | ScanDescription stored with the scan |
| scan_type | – | – | ScanType, e.g. Full, SIM or MSn |
| single_processing_delay_s | number | – | Hold further custom scans this long (ICustomScan.SingleProcessingDelay) |
| Name | Type | Req | Description |
|---|---|---|---|
| custom_scans_last_minute | – | – | – |
| message | string | yes | – |
| running_number | integer | yes | – |
| sent | boolean | yes | True if IAPI reports the command was sent to the instrument |
| values | object | yes | The exact IAPI scan values sent |
No examples provided.
wait_for_scan Wait For Scan ~170
Wait for the next scan that arrives after this call (optionally of one MS order, or the result of a custom scan by its access id) and return it. For a custom scan placed with submit_custom_scan, a result that arrived since it was placed is returned at once. Returns found=false after timeout_s if nothing matching arrived (e.g. the instrument is in Standby).
| Name | Type | Req | Description |
|---|---|---|---|
| access_id | – | – | Only scans with this access id (-1 = system scans) |
| include_header_trailer | boolean | – | Include the raw header and trailer |
| max_centroids | integer | – | Most intense centroids to return per scan |
| ms_order | – | – | Only scans of this MS order (1 = MS1) |
| timeout_s | number | – | Longest time to wait |
| Name | Type | Req | Description |
|---|---|---|---|
| found | boolean | yes | – |
| message | string | yes | – |
| scan | – | yes | – |
| waited_s | number | yes | – |
No examples provided.
What is the Thermo Orbitrap (Instrument API) MCP server?
Thermo Orbitrap (Instrument API) is an MCP server listed in the public MCP registry as io.github.K-Dense-AI/labmcp-thermo-iapi. MCP server adapter for Thermo Fisher Orbitrap mass spectrometers via the licensed Instrument API. This page covers its PyPI package (labmcp-thermo-iapi).
Is the Thermo Orbitrap (Instrument API) MCP server safe to use?
Thermo Orbitrap (Instrument API) scores 83 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 30 September 2026. Its build provenance is signed and verified. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.
What tools does the Thermo Orbitrap (Instrument API) MCP server expose?
Thermo Orbitrap (Instrument API) exposes 15 tools: get_connection_info, get_command_log, reconnect, get_instrument_status, get_possible_scan_parameters, and 10 more. Their descriptions and schemas cost roughly 1,638 tokens of context every time the server is loaded.
Is the Thermo Orbitrap (Instrument API) MCP server still maintained?
Thermo Orbitrap (Instrument API) is still listed as active in the MCP registry. We last reached this channel on 30 September 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.
What licence is the Thermo Orbitrap (Instrument API) MCP server under?
Thermo Orbitrap (Instrument API) declares the Apache-2.0 licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.