Mascot Parser Skill

Version: 1.0.0  |  License: Apache-2.0

An Agent Skill that teaches AI coding assistants how to write scripts against the Mascot Server msparser SDK (Python, Perl, Java, C#).

The skill itself is just markdown — skills/mascot-parser/SKILL.md plus reference files in skills/mascot-parser/references/. It does not contain or redistribute the licensed msparser SDK.

What it covers

• msparser API surface across all four language bindings
• Common recipes: reading .dat results, search submission, server config
• Safety rules (e.g. never submit writes against the public Matrix Science server)
• Cross-language constructor / constant / import differences

Prerequisites

You still need the msparser SDK to actually run any code the assistant writes. Download it from: https://www.matrixscience.com/msparser_download.html

The skill tells the assistant where the bindings live inside the extracted SDK.

Install — Claude Code

Pick one location depending on whether you want the skill globally or per-project.

Windows (PowerShell)

Globally (all projects):

git clone https://github.com/Matrix-Science/mascot-parser-skill.git
New-Item -ItemType Directory -Force "$env:USERPROFILE\.claude\skills" | Out-Null
Copy-Item -Recurse mascot-parser-skill\skills\mascot-parser "$env:USERPROFILE\.claude\skills\"

Per project (run from your project's root):

New-Item -ItemType Directory -Force .claude\skills | Out-Null
Copy-Item -Recurse "C:\path\to\mascot-parser-skill\skills\mascot-parser" .claude\skills\

If you'd rather not use the command line, you can simply clone or download the repo from GitHub in File Explorer and copy the skills\mascot-parser folder into either:

• %USERPROFILE%\.claude\skills\ (global), or
• <your-project>\.claude\skills\ (per-project)

macOS / Linux (bash)

Globally:

git clone https://github.com/Matrix-Science/mascot-parser-skill.git
mkdir -p ~/.claude/skills
cp -r mascot-parser-skill/skills/mascot-parser ~/.claude/skills/

Per project:

mkdir -p .claude/skills
cp -r /path/to/mascot-parser-skill/skills/mascot-parser .claude/skills/

After install

Restart Claude Code (or start a new session). The skill auto-loads when you mention msparser, Mascot Server, .dat files, peptide/protein search results, etc. You can also force it with /skill mascot-parser.

Install — other AI coding tools

The skill format follows Anthropic's Agent Skills spec, which several tools now support:

Tool	Supported	Install location (Windows / Unix)
Claude Code (CLI / desktop / IDE plugins)	yes	%USERPROFILE%\.claude\skills\ or .claude\skills\ (project)
Claude API / Agent SDK	yes	Pass via the Skills API or bundle with your agent
GitHub Copilot CLI	yes (auto-discovered from installed plugins)	Plugin's skills\ directory
Gemini CLI	yes (loaded via activate_skill)	%USERPROFILE%\.gemini\skills\
Cursor / Windsurf / Cline / Aider / etc.	no native skill loader	See "Manual use" below

Manual use (any assistant)

For tools that don't yet support the skill format, the SKILL.md is just a long-form prompt. You have two options:

1. Paste it in — open skills/mascot-parser/SKILL.md and paste the contents into the chat / system prompt.
2. Reference it as context — most assistants let you @-mention or attach files. Point at skills/mascot-parser/SKILL.md and the relevant references/*.md for the language you're using.

The references are split by language (perl-api.md, java-api.md, csharp-api.md) plus common-recipes.md, api-classes.md, and server-config.md, so you can attach only what you need.

Using the skill

Once installed, just ask in plain language. Examples:

• "Write a Python script that loads results.dat and exports peptide hits with score > 30 to CSV."
• "In Perl, list all enzymes configured on my Mascot server."
• "Show me the C# equivalent of ms_searchparams.setLICENSE(...)."
• "Submit an MGF as a Mascot search using the Java bindings."

The skill will guide the assistant on correct API names, language-specific syntax (e.g. C# _params() vs Python params()), and safety constraints.

Credentials in your own project

The skill steers the assistant toward loading Mascot credentials from environment variables or a .env file. A minimal .env looks like:

MASCOT_USER=your-username
MASCOT_PASS=your-password
MASCOT_URL=https://your-mascot-server/mascot/cgi

Make sure your project's .gitignore excludes .env so you don't accidentally commit your Mascot login:

.env
.env.local

Repo layout

skills/mascot-parser/
  SKILL.md              # main skill (Python is the default binding)
  references/
    perl-api.md
    java-api.md
    csharp-api.md
    api-classes.md      # cross-binding class reference
    common-recipes.md
    server-config.md
    obsolete-examples.md

The msparser/, Documentation/, and mascot server scripts/ directories are gitignored — they hold the licensed SDK and are not redistributed.

License

The skill content in this repository (the markdown under skills/ and the documentation files at the repo root) is licensed under the Apache License, Version 2.0 (Apache-2.0). See LICENSE for the full text.

The msparser SDK itself is not covered by this license — it is proprietary software licensed separately by Matrix Science. You must obtain it from https://www.matrixscience.com/msparser_download.html under its own terms.