turnover

turnover calculates protein turnover rates from metabolic-labeling mass spectrometric proteomics data by performing isotopologue demultiplexing, precursor-pool correction, and statistical analysis to quantify synthesis and degradation dynamics.

Key Features:

• Skyline integration: Operates as an external tool for Skyline to process mass spectrometric proteomics data.
• Isotopologue Demultiplexing: Separates isotopic label patterns to measure incorporation of labeled amino acids over time.
• Precursor-Pool Correction: Adjusts for variations in precursor ion pools to improve quantification of labeled peptide fractions.
• Statistical Analysis: Performs statistical analyses to estimate turnover rates and compare differential changes between treatment groups.
• Data Reporting and Visualization: Generates quantitative reports and visualizations of turnover curves and derived parameters.
• Mass spectrometric compatibility: Compatible with various mass spectrometric platforms used in metabolic labeling proteomics.

Scientific Applications:

• Aging: Quantifies changes in protein synthesis and degradation associated with aging.
• Neurodegeneration: Investigates alterations in protein turnover related to neurodegenerative disease processes.
• Skeletal Muscle Atrophy: Analyzes muscle protein dynamics during atrophy.

Methodology:

Isotopologue demultiplexing, precursor-pool correction, statistical analysis, and generation of reports and visualizations; implements previously validated methods for calculating turnover rates and assessing differential changes between treatment groups and is compatible with various mass spectrometric platforms.