apt-spectrum

name	apt-spectrum
description	Create a mass spectrum from loaded atom probe data and optionally identify ions. Use when the user wants to see or analyze a mass spectrum.
argument-hint	[element1 element2 ...]

Create a mass spectrum from the pos variable in the MATLAB workspace. Use the MATLAB MCP server.

Steps

1. Plot the mass spectrum

spec = massSpecPlot(pos, 0.01, 'normalised');

Use bin width 0.01 Da and normalised mode by default. If the user requests different settings, adjust accordingly.

2. Identify ions (if elements provided)

If the user specified elements as $ARGUMENTS, add ion markers for each element. For each element, try common charge states (typically 1+ and 2+ for most elements, 3+ for transition metals):

ionAdd(spec, 'Fe', 2, isotopeTable, colorScheme);
ionAdd(spec, 'Fe', 1, isotopeTable, colorScheme);

If no elements are specified, just show the spectrum and ask the user which elements they expect in their sample. Suggest looking at the major peaks for identification.

3. Report

Tell the user:

• The spectrum is displayed in the MATLAB figure
• Which ions were identified (if any)
• Suggest next steps: identify more ions with /apt-spectrum element1 element2, or define ranges with rangeAddAll

Notes

• isotopeTable and colorScheme must be in the workspace (from /apt-setup)
• If they're missing, load them first:

  load('isotopeTable_naturalAbundances.mat');
  load('colorScheme_default.mat');