DeuteRater

DeuteRater quantifies peptide isotope distributions from D2O-labeled mass spectrometry data to improve concentration and protein turnover rate calculations.

Key Features:

• Isotope Distribution Analysis: Compares observed isotopic envelopes from D2O-labeled peptides to theoretical, label-dependent isotope abundance predictions to quantify peptide incorporation and infer synthesis and degradation rates.
• Neutromer Spacing Utilization: Analyzes changes in neutromer spacing within peptide isotopic envelopes to refine interpretation of isotope incorporation patterns.
• Noise Reduction and Confidence Enhancement: Integrates combined measurements across the isotopic envelope to filter noise and increase confidence in protein turnover estimates.
• Optimization of Data Acquisition Parameters: Evaluates accuracy and precision of peptide measurements to assess the impact of mass spectrometry instrument parameters and data processing steps on turnover estimates.
• Supporting Data: References supporting datasets in the Chorus Project (project 1147) and intermediate calculation files reported as Tables S3 and S4 for reproducibility.

Scientific Applications:

• Kinetic Proteomics: Estimation of protein synthesis and degradation rates from D2O metabolic labeling and mass spectrometry-derived peptide isotopic envelopes.
• Experimental Design and Parameter Optimization: Determination of optimal mass spectrometry acquisition and data processing parameters by evaluating measurement accuracy and precision for peptide-level turnover analysis.

Methodology:

Analyzes isotopic envelopes from D2O-labeled samples by comparing observed isotope distributions and neutromer spacing to theoretical, label-dependent predictions, calculating peptide and protein turnover rates and assessing measurement accuracy and precision.