ICPL_ESIQuant

ICPL_ESIQuant performs quantitative analysis of ESI-MS/MS datasets from Isotope-Coded Protein Labeling (ICPL) experiments to generate peptide- and protein-level quantification for comparative proteomics.

Key Features:

• Vendor-agnostic data processing: Processes mass spectrometric data from multiple instrument vendors.
• Mascot integration: Utilizes Mascot search results to generate detailed protein and peptide result tables from .dat files.
• Support for ICPL multiplexing: Handles ICPL duplex, triplex, and quadruplex experiments.
• Input formats: Accepts MS raw data in .mzXML format and Mascot search results in .dat format.
• ICPL quantification: Quantifies proteins labeled using the ICPL method at peptide and protein levels.
• Comprehensive feature detection: Reports detected, sequenced, and identified features present in the sample.
• Shotgun and directed proteomics support: Supports shotgun and directed strategies and accepts mass inclusion lists to identify peptides not fragmented in the first MS cycle.

Scientific Applications:

• Quantitative proteomics: Measures protein abundance changes across experimental conditions using ICPL labeling and ESI-MS/MS data.
• Biomarker discovery: Enables identification and quantification of candidate protein biomarkers across samples.
• Comparative proteomics and disease progression analysis: Compares proteome alterations between conditions or disease states using multiplexed ICPL experiments.

Methodology:

Processes ESI-MS/MS .mzXML raw data together with Mascot .dat search results to generate protein and peptide result tables, and quantifies ICPL-labeled proteins for duplex, triplex, and quadruplex experiments while supporting shotgun and directed proteomics via mass inclusion lists.