MaXIC-Q

MaXIC-Q performs quantitative analysis of mass spectrometry-based proteomics data using stable isotope labeling (SILAC and ICAT) to compute peptide and protein ratios for differential expression studies.

Key Features:

• Supported labeling techniques: Supports stable isotope labeling by amino acids in cell culture (SILAC), isotope-coded affinity tag (ICAT), and user-developed labeling methods for relative quantitation.
• Input formats and integration: Accepts mzXML spectral files and integrates identification results from SEQUEST, Mascot, and ProteinProphet.
• Elution profile construction: Constructs Projected Ion Mass Spectrum (PIMS) and Extracted Ion Chromatogram (XIC) elution profiles for each ion from mass spectrometry data.
• PIMS validation: Implements a stringent validation procedure on PIMS to eliminate interference from co-eluting peptides and noise.
• Quantitation calculations: Uses areas under XIC curves to determine ion abundances and to calculate peptide and protein ratios.
• Large-scale dataset analysis: Operates on large-scale proteomics datasets to perform systematic quantitation.
• Output generation: Produces visualization diagrams and comprehensive quantitation reports for result inspection.

Scientific Applications:

• Quantitative proteomics: Derives relative peptide and protein abundances from SILAC- and ICAT-labeled mass spectrometry experiments.
• Differential expression analysis: Computes peptide and protein ratios for comparative analysis across biological samples or conditions.
• Interference detection and validation: Detects and excludes co-eluting peptide interference via PIMS validation to improve quantitation accuracy.
• Integrated identification-quantitation workflows: Combines SEQUEST, Mascot, and ProteinProphet identifications with quantitative profiles for downstream analysis.

Methodology:

Constructs PIMS and XIC elution profiles from mzXML mass spectrometry data, applies a stringent validation procedure to PIMS to remove interference, determines ion abundances from areas under XIC curves, and calculates peptide and protein ratios while integrating identification results from SEQUEST, Mascot, and ProteinProphet for SILAC and ICAT experiments.