ASAPRatio

ASAPRatio performs automated statistical analysis of protein abundance ratios from stable-isotope labeling experiments (ICAT, cICAT, SILAC) to quantify and compare protein levels in proteomics studies.

Key Features:

• Automated Analysis: Automates statistical evaluation of protein abundance ratios from mass spectrometry datasets.
• Integration with Mass Spectrometry Data: Processes LC-ESI-MS/MS data derived from fragmented and chromatographically separated labeled peptides.
• Stable-Isotope Labeling Compatibility: Supports ICAT, cICAT, and SILAC labeling strategies for differential proteomics.
• Advanced Statistical Methods: Implements Savitzky-Golay smoothing filters, weighted sample statistics, and Dixon's test for outlier detection.
• Error Evaluation and Significance Testing: Estimates errors associated with abundance ratios and assesses statistical significance of changes.
• High Accuracy and Speed: Generates accurate protein abundance ratios efficiently for large proteomic datasets.

Scientific Applications:

• Differential Protein Expression Analysis: Quantifies and compares protein abundance between biological samples using stable-isotope labels and LC-ESI-MS/MS data.
• Complex Component Identification: Identifies specific components within complexes such as the RNA polymerase II transcription complex amid copurifying proteins.

Methodology:

Processes LC-ESI-MS/MS data and applies Savitzky-Golay smoothing filters, weighted sample statistics, Dixon's test for outliers, and error evaluation/significance testing to compute protein abundance ratios.