XTandem Parser

XTandem Parser parses X!Tandem XML search results from MS/MS experiments to extract peptide identifications and construct an object model for downstream proteomics analysis.

Key Features:

• X!Tandem XML parsing: Parses X!Tandem XML result files and extracts structured search-result information.
• Object model construction: Transforms parsed data into a structured object model representing peptide identifications and protein assignments.
• Java implementation: Implemented in Java for cross-platform execution and integration with Java-based bioinformatics workflows.

Scientific Applications:

• Proteomics identification: Enables identification and characterization of peptides and proteins from MS/MS search results.
• Biomarker discovery: Facilitates comparative analysis of peptide identifications for potential biomarker detection.
• Disease mechanism and personalized medicine: Supports studies linking proteomic changes to disease mechanisms and personalized medicine research.

Methodology:

Reads XML output produced by X!Tandem searches and constructs an object model encapsulating the parsed search results; X!Tandem searches match experimental MS/MS spectra against theoretical spectra derived from protein databases.