PeakQuant

PeakQuant quantifies protein abundance from stable isotope-coded mass spectrometric data to support quantitative proteomics and differential expression analysis.

Key Features:

• FindPairs module: Automates determination of protein abundance ratios from stable isotope-coded mass spectrometric data.
• Labeling support: Supports (14)N/(15)N labeling, SILAC (Stable Isotope Labeling by Amino acids in Cell culture), and iTRAQ (Isobaric Tags for Relative and Absolute Quantitation) experimental designs.
• Statistical framework: Applies advanced statistical methods to identify outliers arising from biological and technical variances in replicate experiments and to ensure robust ratio estimates.

Scientific Applications:

• Quantitative proteome analysis: Determination of relative protein abundance across samples using stable isotope strategies.
• Stable isotope-labeled MS experiments: Analysis of data from (14)N/(15)N, SILAC, and iTRAQ labeling workflows.
• Differential protein expression assessment: Evaluation of significance and variance in protein expression including identification of outlier measurements in replicates.

Methodology:

Analyzes stable isotope-coded mass spectrometric data by automating protein abundance ratio calculation and applying advanced statistical methods to detect outliers from biological and technical replicate variance.