MassChroQ

MassChroQ quantifies peptides and proteins from liquid chromatography-mass spectrometry (LC-MS) data to measure peptide and protein abundances for proteomic analyses.

Key Features:

• Versatile Quantification: Supports both label-free and isotopic labelling quantification methods for high- and low-resolution mass spectrometers.
• Data Alignment and Peak Area Integration: Performs chromatographic alignment and quantifies peptides by peak area integration on extracted ion chromatograms.
• Automatic and Manual Targeting: Determines peptides of interest automatically or via specified m/z and retention time values.
• Handling Complex Experiments: Processes large-scale experiments including protein or peptide fractionation workflows such as SDS-PAGE and 2-D LC.
• Configurability and Traceability: Provides configurable processing steps and records processing traceability to support reproducibility.
• Standardized Output Formats: Exports data in open standard formats for integration into proteomic pipelines and statistical analyses.
• Modularity: Employs a modular design to enable integration with other bioinformatics tools.

Scientific Applications:

• Peptide and Protein Quantification: Accurate quantification of peptides and proteins from LC-MS data in both label-free and isotopically labelled experiments.
• Fractionated and Large-Scale Studies: Analysis of complex, fractionated samples generated by SDS-PAGE or 2-D LC in large-scale proteomic experiments.
• Performance Validation: Evaluated on complex label-free datasets from low- and high-resolution mass spectrometers with reported technical coefficient of variation (CV) of 1.4% and correlation coefficient to protein quantity of 0.98.

Methodology:

Chromatographic alignment, extraction of ion chromatograms, and peptide quantification by peak area integration.