QFAB operates a licensed (MatrixScience) Mascot server at mascot.qfab.org. Mascot allows searches against the popular SwissProt database with peptide mass fingerprints or MS data. Matches are evaluated statistically by comparing observed and calculated peptide fragments.
Searches are submitted by registered users via a web page.
ProteinPilot (SCIEX) is a proprietary software suite that facilitates protein identification and quantitation with particular regard to various peptide modifications and non-tryptic cleavages. Isoforms and protein subsets may be distinguished and it allows a high degree of user control such as suppression of false positives and visualization peptide-protein associations and relationships. ProteinPilot support the generic input for non-SCIEX instruments via .mgf format and is compatible with all proteomics MS/MS systems.
ProteinPilot is accessed via VPN and RDP (Remote Desktop Protocol) to QFAB’s Protein Pilot software.