Compound Discoverer 1.0 Data Review Quick Start

Importance of Topic

In modern analytical laboratories, efficient review and interpretation of complex mass spectrometry data are essential for accurate compound identification and quantification. Compound Discoverer 1.0 offers an integrated environment for rapid visualization of chromatograms, mass spectra and tabular summaries, empowering researchers to validate automated results, integrate manual corrections, and apply advanced fragment annotation workflows without requiring an active software license.

Study Goals and Overview

The guide for Compound Discoverer 1.0 Data Review Quick Start is designed to walk users through the steps necessary to open result files, navigate key graphical interfaces, inspect master tables, and apply custom explanations and FISh scoring. The primary objectives are to ensure that analysts can:

• Access and explore results through independent Chromatogram and Mass Spectrum views.
• Review and filter tabular outputs such as Consolidated Peaks and Compound Hits.
• Integrate manual peak selections when needed.
• Assign custom structural annotations and evaluate Fragment Ion Search coverage.

Methodology and Instrumentation

The workflow operates on .cdResult files generated by processing nodes such as Unknown Detector, Expected Finder, Peak Consolidator and FISh Tracer. Key methodological elements include:

• Floating Views: Chromatogram, Mass Spectrum, Filters, Scatter and Summaries can be detached and resized across multiple monitors.
• Chromatogram View: Displays extracted ion, total ion, base peak, analog or pattern traces based on selected table rows. Users can overlay multiple traces and perform manual integration of peaks.
• Mass Spectrum View: Presents an MS1 spectral tree alongside data‐dependent (DDF) or all‐ion fragmentation (AIF) scans with optional FISh annotation to highlight matched fragment structures.
• Result Filters: A flexible tree structure allows multi‐property AND/OR filtering and persistent filter saving with .filterset files.

Instrumentation details relevant to data acquisition include liquid chromatography coupled to Thermo Scientific mass spectrometers, optionally equipped with UV-Vis or photodiode array detectors for analog traces. Fragment Ion Search (FISh) Scoring leverages theoretical fragment libraries to annotate peaks and compute coverage metrics.

Main Results and Discussion

Users can sort and filter master tables to highlight key compounds, compare control versus sample detections, and resolve ion conflicts between detection nodes. Manual peak integration creates entries in a dedicated Manual Peaks table, while custom explanations attach MOL file structures or drawn formulas to Expected and Unknown Hits. The FISh Scoring node calculates coverage scores by comparing observed centroids against theoretical fragments and displays both per‐scan and composite scores. Mirror plots facilitate visual comparisons of reference and target spectra. The workflow summary view documents the entire pipeline from initial detection through FISh analysis.

Benefits and Practical Applications

By combining automated processing with intuitive graphical inspection and manual override capabilities, Compound Discoverer 1.0 enhances quality control in metabolite profiling, impurity screening and targeted small molecule research. Key advantages include:

• License‐free result exploration for collaborative review or training.
• Rapid identification of false positives through integrated filtering and ion conflict checks.
• Customizable compound annotations linking spectral data to chemical structures.
• Objective fragment scoring improving confidence in compound assignment.

Future Trends and Opportunities

Advancements may include cloud‐based collaboration, machine learning-driven peak detection and annotation, expanded fragment libraries, and tighter integration with laboratory information management systems (LIMS). Automated prioritization of unknowns for structural elucidation and real-time decision support during acquisition represent additional potential developments.

Conclusion

Compound Discoverer 1.0 provides a comprehensive platform for post-processing review of chromatographic and mass spectrometric data. Its flexible views, powerful filtering, manual integration options and FISh Scoring capabilities deliver a robust framework for accurate compound identification and data validation in a wide range of analytical applications.