VIQoR

VIQoR accepts peptide quantitative data from labeled and label-free experiments and accomplishes relative protein quantification with interactive visualization modules for integrating protein with peptide quantitative data including post-translational modifications.

Key Features:

• Protein Inference: Implements two parsimonious algorithms to solve the protein inference problem, with demonstrated ability to handle degenerate peptides.
• Protein Summarization: Uses fast-FARMS factor analysis algorithm followed by a weighted average summarization function that minimizes the effect of missing values.
• Global Correlation Indicator: Optimizes summarization and increases accuracy of quantitative analysis in datasets with replicated design.
• Interactive Visualization: Includes the novel VIQoR plot and visualization modules for integrating protein with peptide quantitative data including post-translational modifications.

Scientific Applications:

• Bottom-up Mass Spectrometry Proteomics: Supports relative protein quantification from peptide quantifications between different biological samples in both labeled and label-free experiments.
• Post-identification Analysis: Provides post-identification quantitative analysis of proteins with simultaneous interactive visualization for data browsing and inspection.

Methodology:

VIQoR implements two parsimonious algorithms for protein inference and uses fast-FARMS factor analysis algorithm followed by a weighted average summarization function for protein abundance summarization, with optimization by the Global Correlation Indicator.