Chromascope can be driven by an AI assistant. You keep working in the Chromascope window; the assistant does the clicking you would otherwise do, by sending commands over a standard called MCP (Model Context Protocol). You say what you want in plain words, the assistant picks the steps, and Chromascope does the numerical work and shows the result in your window.
Four things stay true however you use it:
Chromascope contains no AI. The assistant is a separate program of your choice (for example Claude Desktop). It reasons; Chromascope calculates. Every area, every calibration and every QC verdict is computed by the same code that the buttons use, so a number from the assistant is the number you get by clicking.
You decide what the assistant may do. When you start the program you give it permissions with launch flags. With none, the assistant can only look at files inside the folders you name.
Everything is recorded. The status bar of the chromascope-mcp window says AI connected with the number of requests. The link View log opens the AI call log, which lists every call with its exact request, as it happens. The log lasts only while the window is open; for a permanent record ask the assistant for session_audit or prepare_analysis_report.
The assistant proposes, you approve. Ask it to propose a change instead of making it, and the proposal appears in your window under Audit package, Review AI proposals, with its reason and evidence. Only your click on Approve changes a result. See Reviewing AI proposals.
Look: open files inside the named folders, extract traces, read spectra, preview integrations, read results. Nothing in the window changes.
--allow-changes
Change what is in the window: select, zoom, lay out, apply integrations, run a batch, open methods, sessions and projects, change preferences.
--allow-exports
Write new files: figures, CSV tables, methods, sessions, batches, presets, audit packages. Existing files are never overwritten.
--allow-project-writes
Create projects, save revisions, keep review proposals in a project, approve and commit review proposals stored in a project.
A proposal needs none of the last three flags: showing a proposal changes no result, and approving it in the window is your own action.
--allow-root is needed for everything: it names the folders the assistant may use, and nothing outside them can be read or written. Details and recommendations are in Setup.
The last column says which launch flag the tool needs. "read" means --allow-root alone. A tool with two entries needs the second one only for the extra effect named.
These use the shared analysis engine. The assistant starts a job with start_analysis, follows it, and reads the stored result page by page. With --allow-changes a finished calibration or QC study also appears in the Quantification and QC tab; without it the result stays with the assistant and the window does not show it.
The assistant can
Tools
Flag
read the full list of engine operations, their units and the six workflow recipes
analysis_capabilities
read
start a calibration, quantification or QC job, follow it, read it and cancel it
read an existing project and prepare a report draft from it (nothing is written)
inspect_project, export_project_report
read
open a project in the window, or reload it
open_project, refresh_project
--allow-changes
create a project, or save a new revision
create_project, save_project
--allow-project-writes
build an audit package in a new folder
build_bundle
--allow-exports
check a package, or recompute a stored result and compare it
verify_bundle, reprocess_result
read
keep a review proposal in a project so it can be reviewed later (also in chromascope.exe), approve or reject one that is stored in a project, commit a job to a project
Choose the msconvert program. Picking the executable that converts vendor files decides which program Chromascope runs. That is the operator's decision (the environment variable CHROMASCOPE_MSCONVERT or the window's menu), never an assistant's. open_files and list_mzml_files only report whether a converter is configured.
Mark a peak as reviewed by a human.review_quantification can correct boundaries, but it refuses to set the reviewed state. Only you can press ✓ Accept peak, so a reviewed peak always means a person looked at it.
Approve its own proposal in your window. The buttons Approve and Reject exist only in the window. A proposal appears there through a private route that only a proposal the program itself made can use.
Turn a failing QC rule into a pass. An acknowledgement records a reason; the verdict stays.
Touch anything outside the --allow-root folders. Paths are resolved before they are used, so .. and shortcuts cannot escape. Without a root nothing can be opened.
Overwrite a file. Exports create new files only.
Put a result into the window by itself. Calibration and QC results reach the window through a private route that only a finished engine job uses. Proposals reach the review list the same way.
Run a shell, or use the network.
Use unfinished workflows. Identification, untargeted analysis and statistics are hidden in the standard build.
Some clients accept only about 40 tools. Start chromascope-mcp with --tool-profile core and it lists only 40 tools for the main workflows. A call to any other tool is refused with a message that names the flag to use. These tools are not in the core profile: