Multi-Q

Multi-Q performs multiplexed quantitation of iTRAQ-labeled shotgun proteomic datasets to measure relative protein expression across biological samples.

Key Features:

• Fully Automated Analysis: Processes large volumes of spectral data from iTRAQ experiments and accepts outputs from multiple search engines and mass spectrometer manufacturers.
• Signature Peak Processing: Performs peak detection, background subtraction, isotope correction, and normalization of iTRAQ signature peaks for accurate peptide quantitation.
• Customizable Data Filtering: Applies user-defined thresholds using semiempirical values or statistical models to filter data and ensure statistically meaningful peptide ratio fold changes across instruments with varying dynamic ranges.
• High Accuracy and Throughput: Automates peptide ratio calculation and normalization for large-scale quantitation and has been evaluated using a mixture of 10 standard proteins and human Jurkat T cells showing agreement with expected protein ratios.

Scientific Applications:

• Protein profiling: Quantitative comparison of relative protein expression across conditions using iTRAQ-labeled shotgun proteomics.
• High-throughput quantitative proteomics: Large-scale studies requiring automated peptide ratio calculation, normalization, and isotope correction.
• Biomarker discovery and disease studies: Identifying differential protein expression associated with disease progression or therapeutic interventions.
• Systems and molecular biology: Integration of relative protein abundance measurements into molecular and systems-level analyses.

Methodology:

Processes spectral data from iTRAQ experiments and outputs from multiple search engines/mass spectrometers; performs peak detection, background subtraction, isotope correction, normalization, threshold-based filtering using semiempirical or statistical models, and computes peptide ratios and fold changes.