Introduction
The document introduces MetaboliteTools 1.1, a software package designed for the identification and analysis of metabolites and small molecules using mass spectrometry techniques. It highlights the importance of identifying metabolic changes in drug discovery and the utility of LC-MS, particularly API-oa-TOF and ion trap mass spectrometry, in these studies.

Software Modules
MetabolitePredict: This module predicts possible metabolites based on biotransformation rules applied to a parent drug. It includes a wide range of predefined rules and allows users to create additional rules using the StrucEd program. Results are displayed as a metabolite tree, showing relationships and structures, with molecular formulae and weights calculated automatically.
MetaboliteDetect: This module compares two full scan LC-MS chromatograms using the eXpose algorithm to detect metabolites. It generates a delta chromatogram to identify and assign peaks, allowing for targeted MSn experiments.

Key Features

• Processing of esquire and micrOTOF data
• Creation of expected mass lists
• Difference calculation with eXpose
• Automated creation of EIC traces of detected metabolites
• Peak detection and integration algorithms
• Creation of MRM and autoMSn methods with time segments
• Copy-paste functionality for tables and graphics

Software and Hardware Configurations
The software is compatible with Windows 2000 (SP 4) and Windows XP (SP1). It has been tested with Compass 1.0, HyStar 3.0, esquireControl 5.2, micrOTOF Control 1.0, and DataAnalysis 3.2. Hardware testing included the HCT ion trap, Agilent 1100 HPLC system, and HP Laserjet 2200 printer. Some functionalities are limited when using esquire2000 or esquire4000.

Conclusion
MetaboliteTools 1.1 provides a comprehensive solution for the prediction and detection of metabolites, leveraging the strengths of mass spectrometry techniques to deliver detailed molecular and structural information.