MFPaQ

MFPaQ parses Mascot output and quantifies isotopic labeling-based proteomics data (ICAT, SILAC) from nano-LC-MS/MS to enable comparative peptide and protein abundance analysis.

Key Features:

• Integration with Mascot: Parses Mascot search results and organizes protein identifications based on Mascot score, number of identified peptides, peptide scores, and ranks.
• Quantitative Data Extraction: Extracts quantitative information directly from raw nano-LC-MS/MS files to calculate peptide ratios for comparative proteomic analysis.
• Data Validation and Clustering: Validates identified proteins and clusters them based on quantitative metrics to support interpretation of expression changes.
• Non-redundant Protein List Generation: Generates non-redundant protein lists from multisearch experiments and computes averaged, normalized protein ratios.

Scientific Applications:

• Endothelial cell membrane proteomics: Applied to analysis of membrane proteins from primary human endothelial cells (ECs), including ICAT-labeled microsomal fractions processed by nano-LC-MS/MS and Mascot.
• Differential proteomics of inflammation: Enabled identification of over 600 unique proteins and quantitative differential analysis after EC membrane stimulation with tumor necrosis factor-alpha, interferon-gamma, and lymphotoxin alpha/beta to reveal inflammation-regulated membrane proteins.

Methodology:

Parses Mascot output and integrates quantitative data extracted from nano-LC-MS/MS for isotopic labeling experiments (ICAT, SILAC) to compute peptide and protein ratios, perform validation and clustering, and generate averaged, normalized protein lists.