How do I install the Ms Spectra Simulation skill?

Run npx skillmds@latest add internscience/ms-spectra-simulation in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Ms Spectra Simulation safe to use?

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Which AI agents work with Ms Spectra Simulation?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Ms Spectra Simulation free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Ms Spectra Simulation?

internscience (@internscience) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Ms Spectra Simulation by internscience

Name: Ms Spectra Simulation
Author: internscience

Ms Spectra Simulation

Predict and visualize MS/MS spectra from a single SMILES using the fioRa online app. Use when the user wants a mass spectrum, MGF/MSP output, or a plotted stick spectrum from SMILES, with optional custom Name, precursor type, collision energy, and instrument settings.

internscience 7ae6bf5 88 files · 176.7 MB Updated Sep 17, 2026

File contents

MS Spectra Simulation Skill

When to use this

Use this skill when the user provides a SMILES string and wants:

Predicted MS/MS spectrum
Raw MSP output downloaded from fioRa
Standard MGF output
A quick stick-spectrum PNG visualization
Simple defaults without manually preparing a CSV

Inputs

SMILES string (required)
--name (optional, default: mol1)
--precursor (optional, default: [M+H]+)
--ce (optional, default: 20)
--instrument (optional, default: HCD)
--output-stem (optional, default: predicted_ms)
--plot / --no-plot (optional, default: plot enabled)
--show-title / --no-show-title (optional, default: no title on the plot)

Outputs

/tmp/chemclaw/predicted_ms.msp
/tmp/chemclaw/predicted_ms.mgf
/tmp/chemclaw/predicted_ms.png

If --output-stem mol1 is used, the outputs become:

/tmp/chemclaw/mol1.msp
/tmp/chemclaw/mol1.mgf
/tmp/chemclaw/mol1.png

Agent response

When returning results to the user, include the generated spectrum image directly in the response when a PNG was created.

Notes

This skill calls the fioRa online app at https://apps.bam.de/shn01/fioRa/.
The site is a Shiny web app, so this skill uses Playwright browser automation instead of a simple REST request.
Network access is required.

New environment (from zero)

conda create -n fiora-online python=3.10 pip -y
conda activate fiora-online

cd ms-spectra-simulation
python -m pip install -r requirements.txt
python -m playwright install chromium
python ms_spectra_simulation.py CCO

Run the script in an environment with browser access.

How to use (environment already prepared)

Fastest default run

cd ms-spectra-simulation
python ms_spectra_simulation.py CCO

This uses:

name=mol1
precursor=[M+H]+
ce=20
instrument=HCD
plot enabled
plot title hidden
fioRa online backend

Custom metadata

cd ms-spectra-simulation
python ms_spectra_simulation.py "CCO" \
  --name mol1 \
  --precursor "[M+H]+" \
  --ce 20 \
  --instrument HCD

Keep the spectrum but skip PNG

cd ms-spectra-simulation
python ms_spectra_simulation.py "CCO" --no-plot

Show the title on the figure

cd ms-spectra-simulation
python ms_spectra_simulation.py "CCO" --show-title

---name: ms-spectra-simulationdescription: Predict and visualize MS/MS spectra from a single SMILES using the fioRa online app. Use when the user wants a mass spectrum, MGF/MSP output, or a plotted stick spectrum from SMILES, with optional custom Name, precursor type, collision energy, and instrument settings.---# MS Spectra Simulation Skill## When to use thisUse this skill when the user provides a **SMILES** string and wants:- Predicted **MS/MS spectrum**- Raw **MSP** output downloaded from fioRa- Standard **MGF** output- A quick **stick-spectrum PNG** visualization- Simple defaults without manually preparing a CSV## Inputs- **SMILES** string (required)- `--name` (optional, default: `mol1`)- `--precursor` (optional, default: `[M+H]+`)- `--ce` (optional, default: `20`)- `--instrument` (optional, default: `HCD`)- `--output-stem` (optional, default: `predicted_ms`)- `--plot / --no-plot` (optional, default: plot enabled)- `--show-title / --no-show-title` (optional, default: no title on the plot)## Outputs- `/tmp/chemclaw/predicted_ms.msp`- `/tmp/chemclaw/predicted_ms.mgf`- `/tmp/chemclaw/predicted_ms.png`If `--output-stem mol1` is used, the outputs become:- `/tmp/chemclaw/mol1.msp`- `/tmp/chemclaw/mol1.mgf`- `/tmp/chemclaw/mol1.png`## Agent responseWhen returning results to the user, include the generated spectrum image directly in the response when a PNG was created.## Notes- This skill calls the fioRa online app at `https://apps.bam.de/shn01/fioRa/`.- The site is a Shiny web app, so this skill uses Playwright browser automation instead of a simple REST request.- Network access is required.## New environment (from zero)```bashconda create -n fiora-online python=3.10 pip -yconda activate fiora-onlinecd ms-spectra-simulationpython -m pip install -r requirements.txtpython -m playwright install chromiumpython ms_spectra_simulation.py CCO```- Run the script in an environment with browser access.## How to use (environment already prepared)### Fastest default run```bashcd ms-spectra-simulationpython ms_spectra_simulation.py CCO```This uses:- `name=mol1`- `precursor=[M+H]+`- `ce=20`- `instrument=HCD`- plot enabled- plot title hidden- fioRa online backend### Custom metadata```bashcd ms-spectra-simulationpython ms_spectra_simulation.py "CCO" \ --name mol1 \ --precursor "[M+H]+" \ --ce 20 \ --instrument HCD```### Keep the spectrum but skip PNG```bashcd ms-spectra-simulationpython ms_spectra_simulation.py "CCO" --no-plot```### Show the title on the figure```bashcd ms-spectra-simulationpython ms_spectra_simulation.py "CCO" --show-title```

Frequently asked questions