Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion)
PYPI · LABMCP-MS-DATA · SCANNED SEP 30
MCP server for LC-MS data in mzML/mzMLb and Bruker timsTOF files; vendor formats via msconvert.
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 Security50
- Malware scan not yet available for this package.Unverified
- 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 23 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 Usability65
- AI-judged instruction clarity (excellent).Pass
- Context-footprint check failed: tool/resource definitions use about 2374 tokens (~197/item across 12 items; 12 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 Coverage98
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 95% 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 12 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 13 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 Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) MCP server?
Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) runs locally as a PyPI package, launched with uvx labmcp-ms-data. 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-ms-data
claude mcp add k-dense-ai-labmcp-ms-data -- uvx labmcp-ms-data
{
"mcpServers": {
"k-dense-ai-labmcp-ms-data": {
"command": "uvx",
"args": [
"labmcp-ms-data"
]
}
}
} {
"servers": {
"k-dense-ai-labmcp-ms-data": {
"command": "uvx",
"args": [
"labmcp-ms-data"
]
}
}
} codex mcp add k-dense-ai-labmcp-ms-data -- uvx labmcp-ms-data
{
"$schema": "https://opencode.ai/config.json",
"mcp": {
"k-dense-ai-labmcp-ms-data": {
"type": "local",
"command": [
"uvx",
"labmcp-ms-data"
],
"enabled": true
}
}
} openclaw mcp add k-dense-ai-labmcp-ms-data --command uvx --arg labmcp-ms-data
mcp_servers:
k-dense-ai-labmcp-ms-data:
command: "uvx"
args: ["labmcp-ms-data"] {
"McpServers": {
"k-dense-ai-labmcp-ms-data": {
"Transport": "stdio",
"Command": "uvx",
"Arguments": [
"labmcp-ms-data"
]
}
}
} assistant mcp add k-dense-ai-labmcp-ms-data -t stdio -c uvx -a labmcp-ms-data
{
"mcpServers": {
"k-dense-ai-labmcp-ms-data": {
"command": "uvx",
"args": [
"labmcp-ms-data"
]
}
}
} 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.
- 28 Sept 26 +26
- 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 −29
- 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 69
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-ms-data@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-ms-data-v0.1.1 |
| Rekor log index | 2969517783 |
| Predicate type | PyPI publish attestation https://docs.pypi.org/attestations/publish/v1 |
| Subject digest | sha256:c3853ad809b652cf37bb6d5a1aeefb0383d43f7ceb3eca4e3a9d6974f991d68d |
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 23 packages
| Packages resolved | 23 |
|---|---|
| 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 →
convert_to_mzml Convert To Mzml ~225
Convert a vendor file (Thermo .raw, Waters .raw, Agilent .d, SCIEX .wiff, Shimadzu .lcd, Bruker .d) to mzML with the converter the user installed (ThermoRawFileParser, ProteoWizard msconvert, or msconvert in Docker; chosen with --option converter=...). Writes a new file in the data folder. Can take minutes; fails with install instructions if no converter is set up.
| Name | Type | Req | Description |
|---|---|---|---|
| dry_run | boolean | – | Only show the command that would be run |
| gzip | boolean | – | Write .mzML.gz |
| output_folder | – | – | Folder for the .mzML, inside the data folder (default: next to the input) |
| overwrite | boolean | – | Replace an existing output file |
| path | string | yes | Vendor file or folder (from list_runs), relative to the data folder |
| peak_picking | boolean | – | Centroid with the vendor algorithm during conversion |
| timeout_s | number | – | Give up after this many seconds |
| Name | Type | Req | Description |
|---|---|---|---|
| command | array | yes | – |
| converter | string | yes | – |
| detected_format | string | yes | – |
| dry_run | boolean | yes | – |
| duration_s | – | yes | – |
| input | string | yes | – |
| log_tail | string | yes | – |
| notes | array | yes | – |
| output | string | yes | – |
| output_size_mb | – | yes | – |
| return_code | – | yes | – |
| success | boolean | yes | – |
No examples provided.
extract_ion_chromatogram Extract Ion Chromatogram ~293
Extracted ion chromatogram (XIC/EIC) for one or more m/z values: the summed intensity within ± tolerance (ppm or Da) in every MS1 spectrum (or another `ms_level`). For each target returns the apex RT and intensity, the apex peak's boundaries, area (intensity x min, no baseline subtraction) and FWHM, plus a downsampled trace. Reads every spectrum in the RT window, so restrict `rt_start_min`/`rt_end_min` on long runs.
| Name | Type | Req | Description |
|---|---|---|---|
| max_points | integer | – | Maximum points returned (downsampled, max per bin) |
| ms_level | integer | – | MS level to use (1 = survey scans) |
| mz | array | yes | Target m/z value(s) |
| overwrite | boolean | – | Allow replacing an existing save_path file |
| path | – | – | Run path relative to the data folder (from list_runs); may be omitted if there is one run |
| rt_end_min | – | – | Only use spectra at or before this RT (min) |
| rt_start_min | – | – | Only use spectra at or after this RT (min) |
| save_path | – | – | Optional new .csv file inside the data folder for the full-resolution data |
| tolerance | number | – | m/z tolerance (± this value) |
| tolerance_unit | string | – | Tolerance unit: ppm or da |
| Name | Type | Req | Description |
|---|---|---|---|
| ms_level | integer | yes | – |
| path | string | yes | – |
| rt_window_min | – | yes | – |
| saved_to | – | yes | – |
| simulated | boolean | yes | – |
| spectra_used | integer | yes | – |
| traces | array | yes | – |
| warnings | array | yes | – |
No examples provided.
find_ms2_scans Find Ms2 Scans ~197
Find the MS2 (MSn) spectra whose precursor m/z is within ± tolerance of `precursor_mz`, optionally within an RT window and for one charge state. Returns index, scan number, RT, precursor m/z, error in ppm, charge and intensity; open any hit with get_spectrum.
| Name | Type | Req | Description |
|---|---|---|---|
| charge | – | – | Only this precursor charge |
| max_results | integer | – | – |
| path | – | – | Run path relative to the data folder (from list_runs); may be omitted if there is one run |
| precursor_mz | number | yes | Precursor m/z to look for |
| rt_end_min | – | – | Only use spectra at or before this RT (min) |
| rt_start_min | – | – | Only use spectra at or after this RT (min) |
| tolerance | number | – | m/z tolerance (± this value) |
| tolerance_unit | string | – | Tolerance unit: ppm or da |
| Name | Type | Req | Description |
|---|---|---|---|
| matches | array | yes | – |
| path | string | yes | – |
| precursor_mz | number | yes | – |
| rt_window_min | – | yes | – |
| simulated | boolean | yes | – |
| tolerance_da | number | yes | – |
| total_matches | integer | yes | – |
| truncated | boolean | yes | – |
No examples provided.
get_bpc Get Bpc ~201
Base peak chromatogram (intensity of the most intense peak per spectrum, with its m/z) vs retention time, downsampled to `max_points`. Cleaner than the TIC for spotting eluting compounds; the base-peak m/z tells you which ion dominates each part of the run.
| Name | Type | Req | Description |
|---|---|---|---|
| max_points | integer | – | Maximum points returned (downsampled, max per bin) |
| ms_level | integer | – | MS level to use (1 = survey scans) |
| overwrite | boolean | – | Allow replacing an existing save_path file |
| path | – | – | Run path relative to the data folder (from list_runs); may be omitted if there is one run |
| rt_end_min | – | – | Only use spectra at or before this RT (min) |
| rt_start_min | – | – | Only use spectra at or after this RT (min) |
| save_path | – | – | Optional new .csv file inside the data folder for the full-resolution data |
| Name | Type | Req | Description |
|---|---|---|---|
| area | – | yes | Trapezoidal integral over RT in minutes (intensity x min) |
| base_peak_mz | – | – | BPC only: m/z of the base peak per point |
| intensity | array | yes | – |
| kind | string | yes | – |
| max_at_rt_min | – | yes | – |
| max_intensity | – | yes | – |
| median_intensity | – | yes | – |
| ms_level | integer | yes | – |
| notes | array | yes | – |
| path | string | yes | – |
| points_returned | integer | yes | – |
| rt_min | array | yes | – |
| saved_to | – | yes | – |
| simulated | boolean | yes | – |
| spectra_used | integer | 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_run_info Get Run Info ~107
Describe one run: instrument vendor/model/serial (when the file records them), acquisition date, software, number of spectra per MS level, retention-time and m/z ranges, polarity, centroid/profile, and whether ion-mobility data is present. The first call on a large file indexes it (can take a while); later calls are instant.
| Name | Type | Req | Description |
|---|---|---|---|
| path | – | – | Run path relative to the data folder (from list_runs); may be omitted if there is one run |
| Name | Type | Req | Description |
|---|---|---|---|
| acquisition_date | – | yes | – |
| format | string | yes | – |
| instrument_model | – | yes | – |
| instrument_serial | – | yes | – |
| instrument_vendor | – | yes | – |
| ion_mobility | boolean | yes | – |
| mz_max | – | yes | – |
| mz_min | – | yes | Lowest observed (or acquisition-range) m/z |
| notes | array | yes | – |
| path | string | yes | – |
| polarity | string | yes | – |
| rt_end_min | – | yes | – |
| rt_start_min | – | yes | – |
| sample_name | – | yes | – |
| simulated | boolean | yes | – |
| software | – | yes | – |
| spectra_by_ms_level | object | yes | – |
| spectra_total | integer | yes | – |
| spectrum_type | string | yes | – |
No examples provided.
get_spectrum Get Spectrum ~284
Read one spectrum, chosen by `index`, `scan_number`, `native_id` or nearest `rt_min` (give exactly one). Returns MS level, RT, polarity, centroid/profile, precursor m/z and charge for MS2, a summary (peak count, TIC, base peak, m/z range) and the `top_n` most intense peaks; `save_path` writes the full peak list to CSV. For profile spectra the top peaks are local maxima of the profile.
| Name | Type | Req | Description |
|---|---|---|---|
| index | – | – | 0-based spectrum index in the file |
| ms_level | – | – | With rt_min: MS level to pick (default 1) |
| mz_max | – | – | Only consider peaks below this m/z |
| mz_min | – | – | Only consider peaks above this m/z |
| native_id | – | – | Exact native spectrum id |
| overwrite | boolean | – | Allow replacing an existing save_path file |
| path | – | – | Run path relative to the data folder (from list_runs); may be omitted if there is one run |
| rt_min | – | – | Pick the spectrum nearest this RT (min) |
| save_path | – | – | Optional new .csv file inside the data folder for the full-resolution data |
| scan_number | – | – | Native scan number (e.g. Thermo scan=N) |
| top_n | integer | – | Number of most intense peaks to return |
| Name | Type | Req | Description |
|---|---|---|---|
| base_peak_intensity | – | yes | – |
| base_peak_mz | – | yes | – |
| filter_string | – | yes | – |
| index | integer | yes | 0-based position in the file |
| injection_time_ms | – | yes | – |
| ms_level | integer | yes | – |
| mz_range | – | yes | – |
| native_id | string | yes | – |
| notes | array | yes | – |
| path | string | yes | – |
| peak_count | integer | yes | – |
| polarity | string | yes | – |
| precursor | – | yes | – |
| rt_min | – | yes | – |
| saved_to | – | yes | – |
| scan_number | – | yes | – |
| simulated | boolean | yes | – |
| spectrum_type | string | yes | – |
| tic | number | yes | Sum of intensities (inside the m/z window, if given) |
| top_peaks | array | yes | Most intense peaks, highest first |
No examples provided.
get_tic Get Tic ~197
Total ion chromatogram (sum of all intensities per spectrum vs retention time) for one MS level, downsampled to `max_points` (keeping the maximum in each bin so peaks survive). Returns the apex, median and area; `save_path` writes every point to CSV.
| Name | Type | Req | Description |
|---|---|---|---|
| max_points | integer | – | Maximum points returned (downsampled, max per bin) |
| ms_level | integer | – | MS level to use (1 = survey scans) |
| overwrite | boolean | – | Allow replacing an existing save_path file |
| path | – | – | Run path relative to the data folder (from list_runs); may be omitted if there is one run |
| rt_end_min | – | – | Only use spectra at or before this RT (min) |
| rt_start_min | – | – | Only use spectra at or after this RT (min) |
| save_path | – | – | Optional new .csv file inside the data folder for the full-resolution data |
| Name | Type | Req | Description |
|---|---|---|---|
| area | – | yes | Trapezoidal integral over RT in minutes (intensity x min) |
| base_peak_mz | – | – | BPC only: m/z of the base peak per point |
| intensity | array | yes | – |
| kind | string | yes | – |
| max_at_rt_min | – | yes | – |
| max_intensity | – | yes | – |
| median_intensity | – | yes | – |
| ms_level | integer | yes | – |
| notes | array | yes | – |
| path | string | yes | – |
| points_returned | integer | yes | – |
| rt_min | array | yes | – |
| saved_to | – | yes | – |
| simulated | boolean | yes | – |
| spectra_used | integer | yes | – |
No examples provided.
list_runs List Runs ~151
Find mass-spectrometry runs in the data folder and detect each one's vendor and format (mzML/mzML.gz/mzMLb, Bruker .d TDF or BAF, Agilent .d, Thermo .raw, Waters .raw folder, SCIEX .wiff/.wiff2, Shimadzu .lcd, mzXML). `readable_directly=false` means the run must be converted with convert_to_mzml before it can be analysed.
| Name | Type | Req | Description |
|---|---|---|---|
| max_results | integer | – | – |
| recursive | boolean | – | Also search subfolders (up to 6 levels) |
| subfolder | string | – | Folder to search, relative to the data folder |
| Name | Type | Req | Description |
|---|---|---|---|
| data_folder | string | yes | – |
| runs | array | yes | – |
| simulated | boolean | yes | – |
| total_found | integer | yes | – |
| truncated | boolean | 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.
summarise_run Summarise Run ~96
Quick QC of a run: MS1/MS2 counts, TIC stability (CV, spray dropouts), where the signal elutes, cycle time, MS2 scans per cycle, median injection times and how often MS2 hit the maximum injection time, and precursor charge states. Returns plain-language warnings.
| Name | Type | Req | Description |
|---|---|---|---|
| path | – | – | Run path relative to the data folder (from list_runs); may be omitted if there is one run |
| Name | Type | Req | Description |
|---|---|---|---|
| median_cycle_time_s | – | yes | Median time between consecutive MS1 scans |
| median_ms1_injection_time_ms | – | yes | – |
| median_ms2_injection_time_ms | – | yes | – |
| ms1_spectra | integer | yes | – |
| ms2_at_max_injection_time_percent | – | yes | – |
| ms2_per_cycle_max | – | yes | – |
| ms2_per_cycle_mean | – | yes | – |
| ms2_per_cycle_median | – | yes | – |
| ms2_precursor_charges | object | yes | – |
| ms2_spectra | integer | yes | – |
| msn_higher_spectra | integer | yes | – |
| path | string | yes | – |
| rt_end_min | – | yes | – |
| rt_start_min | – | yes | – |
| simulated | boolean | yes | – |
| tic_cv_percent | – | yes | Coefficient of variation of the MS1 TIC (whole run) |
| tic_dropout_rts_min | array | yes | – |
| tic_dropouts | integer | yes | MS1 scans with TIC < 20 % of the local median (spray instability) |
| tic_elution_quartiles_min | – | yes | RT at which 25 / 50 / 75 % of the summed MS1 TIC has eluted |
| tic_median | – | yes | – |
| warnings | array | yes | – |
No examples provided.
What is the Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) MCP server?
Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) is an MCP server listed in the public MCP registry as io.github.K-Dense-AI/labmcp-ms-data. MCP server for LC-MS data in mzML/mzMLb and Bruker timsTOF files; vendor formats via msconvert. This page covers its PyPI package (labmcp-ms-data).
Is the Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) MCP server safe to use?
Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) scores 66 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 Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) MCP server expose?
Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) exposes 12 tools: get_connection_info, get_command_log, reconnect, list_runs, get_run_info, and 7 more. Their descriptions and schemas cost roughly 1,872 tokens of context every time the server is loaded.
Is the Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) MCP server still maintained?
Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) 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 Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) MCP server under?
Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) 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.