JS-MS

JS-MS provides capabilities to create, visualize, and edit precursor mass spectrometry ground-truth data for evaluation of MS1-aware algorithms.

Key Features:

• Ground-truth dataset generation: Generates precursor MS ground-truth datasets used for evaluating MS1-aware algorithms in quantitative mass spectrometry workflows.
• Visualization: Presents MS signal data in two-dimensional and three-dimensional formats for inspection of spectral and chromatographic features.
• Annotation tools: Captures, edits, saves, and views isotopic envelope and extracted isotopic chromatogram (XIC) features.
• MsDataServer API integration: Interfaces via HTTP to the MsDataServer API to access MS data stored in the MzTree format.

Scientific Applications:

• Evaluation of MS1-aware algorithms: Provides ground-truth data and visualizations to assess performance, bias, and coverage of MS1-aware feature-finding methods.
• Quantitative mass spectrometry benchmarking: Enables creation of reference datasets for benchmarking algorithm accuracy and statistical significance in quantitative MS workflows.
• Assessment of feature-finding results: Allows inspection and comparison of feature-finding algorithm outputs against annotated isotopic envelopes and XICs.

Methodology:

Creates, visualizes, and edits precursor ground-truth data; captures and manages isotopic envelope and XIC annotations; visualizes MS signal data in 2D and 3D; and accesses MS data via HTTP through the MsDataServer API using the MzTree format.