MSQuant

MSQuant quantifies proteins and analyzes protein–protein interactions by integrating Mascot search results with raw mass spectrometry data from stable isotope labeling by amino acids in cell culture (SILAC).

Key Features:

• Integration of Data Sources: Combines Mascot peptide and protein identifications with raw SILAC-derived mass spectra to enable quantitative comparison.
• Quantitative Proteomics: Determines isotope ratios from mass spectrometry to distinguish protein abundance changes and specific interactions, for example between phosphorylated and non-phosphorylated states.
• Specificity in Protein Interaction Analysis: Supports identification of proteins captured by affinity pull-down experiments using synthetic peptides, including interactions involving SH2 and SH3 modular domains.

Scientific Applications:

• Cell Signaling Studies: Characterizes regulated interactions between short unstructured peptide sequences and signaling domains, for example phosphorylated epidermal growth factor receptor peptides interacting with Grb2.
• Pathway Analysis: Identifies shifts in cellular pathways, such as transitions from Ras-dependent signaling to actin remodeling and endocytic events mediated by proline–SH3 domain switches.

Methodology:

Methods include stable isotope labeling by amino acids in cell culture (SILAC), affinity pull-down experiments using synthetic peptides in active and control states, mass spectrometry analysis to obtain isotope ratios, and integration of Mascot search results with raw mass spectrometry data.