Ariadne

Ariadne performs absolute and relative quantification of Selected Reaction Monitoring (SRM) mass spectrometry data for proteomics analyses.

Key Features:

• Automation and robustness: Fully automates quantification using signal processing and statistical learning methodologies to provide robust performance across diverse SRM datasets.
• Metadata integration: Imports transition lists and uses mProphet outputs to target and filter transitions for accurate quantification.
• External calibration curve method: Employs external calibration curves to estimate absolute protein abundances with linearity over a wide dynamic range.
• Performance benchmarking: Benchmarked against mProphet and Skyline with demonstrated improvements in efficiency, linearity, accuracy, and precision across datasets.
• High discrimination sensitivity: Statistically distinguishes between abundance levels down to 0.1 and 0.2 femtomoles.

Scientific Applications:

• Large-scale SRM differential expression studies: Quantifies multiple proteins across numerous samples to support differential expression analyses in proteomics.
• Absolute abundance estimation: Determines absolute protein concentrations in complex biological samples using external calibration curves.
• Low-abundance detection: Detects and distinguishes subtle changes in protein levels at low femtomolar concentrations (0.1 and 0.2 femtomoles).

Methodology:

Uses advanced signal processing and statistical learning; imports metadata from transition lists and filters transitions using mProphet outputs; applies external calibration curve models for absolute quantification; benchmarking performed against mProphet and Skyline.