Jtraml

Jtraml provides a Java API implementing the Proteomics Standards Initiative's Transitions Markup Language (TraML) specification for representing Selected Reaction Monitoring (SRM) transitions in targeted mass spectrometry.

Key Features:

• Comprehensive API: Provides a complete Java API that encompasses all elements defined in the TraML XSD schema.
• Controlled Vocabulary Support: Includes methods to construct instances based on controlled vocabularies for accurate definition of SRM transitions.
• Two-Way Conversion: Facilitates conversion between TraML documents and vendor-specific files.

Scientific Applications:

• Standardized SRM representation: Encodes Selected Reaction Monitoring (SRM) transitions in TraML for targeted mass spectrometry studies in proteomics.
• Vendor format integration: Enables integration of vendor-specific files into TraML-based analyses and workflows.

Methodology:

Implements the TraML XSD specification in Java and exposes an API covering all schema elements.