Welcome to Paftacular's documentation! Paftacular is a Python library for parsing and serializing mzPAF (Peak Annotation Format). mzPAF is a specification from the Proteomics Standards Initiative (PSI) that provides a compact, human-readable notation for describing fragment ion types, chemical modifications, charge states, mass errors, and confidence scores.

Features

• mzPAF parsing: Handles parsing / serializing of mzPAF strings

• Properties: Supports calculating mass and composition of annotated ions

• Type-Annotations: typed.py file for static type checking

• Caching: serialization and parsing results are cached for performance (when applicable)

• Integrated: Integrated with peptacular, such that peptacular can output mzPAF annotations for fragment ions

Contents:

• Installation
  • Requirements
  • Installing from PyPI
  • Optional Dependencies
  • Installing from Source
  • Development Installation
• Usage
  • Quick Start
  • Basic Peptide Ions
  • Other Ion Types
  • Modifications
  • Isotopes
  • Adducts
  • Charge States
  • Mass Errors and Confidence
  • Complex Annotations
  • Mass Calculations
  • Parsing Multiple Annotations
  • Creating Annotations Programmatically
  • Serialization (Round-trip)
  • Export to Dictionary
  • Peptacular Integration
• API Reference
  • Parser
  • Annotation Types
  • Constants
  • Utilities

Indices and tables

• Index

• Module Index

• Search Page